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comparison InternalCalibration.xml @ 9:4682dcff7e2f draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:23:50 +0000
parents 6b0c27522bcd
children cca2b6c3ae61
comparison
equal deleted inserted replaced
8:657c27a95f63 9:4682dcff7e2f
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="2.3.0"> 4 <tool id="InternalCalibration" name="InternalCalibration" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[InternalCalibration 15 @EXT_FOO@
14 16 #import re
15 #if $param_in: 17
16 -in $param_in 18 ## Preprocessing
17 #end if 19 mkdir in &&
18 #if $param_out: 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 -out $param_out 21 mkdir out &&
20 #end if 22 #if $cal.id_in:
21 #if $param_rscript_executable: 23 mkdir cal.id_in &&
22 -rscript_executable $param_rscript_executable 24 ln -s '$cal.id_in' 'cal.id_in/${re.sub("[^\w\-_]", "_", $cal.id_in.element_identifier)}.$gxy2omsext($cal.id_in.ext)' &&
23 #end if 25 #end if
24 #if $param_ppm_match_tolerance: 26 #if $cal.lock_in:
25 -ppm_match_tolerance $param_ppm_match_tolerance 27 mkdir cal.lock_in &&
26 #end if 28 ln -s '$cal.lock_in' 'cal.lock_in/${re.sub("[^\w\-_]", "_", $cal.lock_in.element_identifier)}.$gxy2omsext($cal.lock_in.ext)' &&
27 29 #end if
28 #if $rep_param_ms_level: 30 #if "lock_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
29 -ms_level 31 mkdir cal_lock_out &&
30 #for token in $rep_param_ms_level: 32 #end if
31 #if " " in str(token): 33 #if "lock_fail_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
32 "$token.param_ms_level" 34 mkdir cal_lock_fail_out &&
33 #else 35 #end if
34 $token.param_ms_level 36 #if "models_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
35 #end if 37 mkdir quality_control_models &&
36 #end for 38 #end if
37 #end if 39 #if "models_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
38 #if $param_RT_chunking: 40 mkdir quality_control_models_plot &&
39 -RT_chunking $param_RT_chunking 41 #end if
40 #end if 42 #if "residuals_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
41 #if $param_cal_id_in: 43 mkdir quality_control_residuals &&
42 -cal:id_in $param_cal_id_in 44 #end if
43 #end if 45 #if "residuals_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
44 #if $param_cal_lock_in: 46 mkdir quality_control_residuals_plot &&
45 -cal:lock_in $param_cal_lock_in 47 #end if
46 #end if 48
47 #if $param_cal_lock_out: 49 ## Main program call
48 -cal:lock_out $param_cal_lock_out 50
49 #end if 51 set -o pipefail &&
50 #if $param_cal_lock_fail_out: 52 @EXECUTABLE@ -write_ctd ./ &&
51 -cal:lock_fail_out $param_cal_lock_fail_out 53 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
52 #end if 54 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
53 #if $param_cal_lock_require_mono: 55 -in
54 -cal:lock_require_mono 56 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
55 #end if 57 -out
56 #if $param_cal_lock_require_iso: 58 'out/output.${gxy2omsext("mzml")}'
57 -cal:lock_require_iso 59 #if $cal.id_in:
58 #end if 60 -cal:id_in
59 #if $param_cal_model_type: 61 'cal.id_in/${re.sub("[^\w\-_]", "_", $cal.id_in.element_identifier)}.$gxy2omsext($cal.id_in.ext)'
60 -cal:model_type 62 #end if
61 #if " " in str($param_cal_model_type): 63 #if $cal.lock_in:
62 "$param_cal_model_type" 64 -cal:lock_in
63 #else 65 'cal.lock_in/${re.sub("[^\w\-_]", "_", $cal.lock_in.element_identifier)}.$gxy2omsext($cal.lock_in.ext)'
64 $param_cal_model_type 66 #end if
65 #end if 67 #if "lock_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
66 #end if 68 -cal:lock_out
67 #if $param_RANSAC_enabled: 69 'cal_lock_out/output.${gxy2omsext("mzml")}'
68 -RANSAC:enabled 70 #end if
69 #end if 71 #if "lock_fail_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
70 #if $param_RANSAC_threshold: 72 -cal:lock_fail_out
71 -RANSAC:threshold $param_RANSAC_threshold 73 'cal_lock_fail_out/output.${gxy2omsext("mzml")}'
72 #end if 74 #end if
73 #if $param_RANSAC_pc_inliers: 75 #if "models_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
74 -RANSAC:pc_inliers $param_RANSAC_pc_inliers 76 -quality_control:models
75 #end if 77 'quality_control_models/output.${gxy2omsext("csv")}'
76 #if $param_RANSAC_iter: 78 #end if
77 -RANSAC:iter $param_RANSAC_iter 79 #if "models_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
78 #end if 80 -quality_control:models_plot
79 #if $param_goodness_median: 81 'quality_control_models_plot/output.${gxy2omsext("png")}'
80 -goodness:median $param_goodness_median 82 #end if
81 #end if 83 #if "residuals_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
82 #if $param_goodness_MAD: 84 -quality_control:residuals
83 -goodness:MAD $param_goodness_MAD 85 'quality_control_residuals/output.${gxy2omsext("csv")}'
84 #end if 86 #end if
85 #if $param_quality_control_models: 87 #if "residuals_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
86 -quality_control:models $param_quality_control_models 88 -quality_control:residuals_plot
87 #end if 89 'quality_control_residuals_plot/output.${gxy2omsext("png")}'
88 #if $param_quality_control_models_plot: 90 #end if
89 -quality_control:models_plot $param_quality_control_models_plot 91 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
90 #end if 92 | tee '$stdout'
91 #if $param_quality_control_residuals: 93 #end if
92 -quality_control:residuals $param_quality_control_residuals 94
93 #end if 95 ## Postprocessing
94 #if $param_quality_control_residuals_plot: 96 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
95 -quality_control:residuals_plot $param_quality_control_residuals_plot 97 #if "lock_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
96 #end if 98 && mv 'cal_lock_out/output.${gxy2omsext("mzml")}' '$cal_lock_out'
97 #if $adv_opts.adv_opts_selector=='advanced': 99 #end if
98 #if $adv_opts.param_force: 100 #if "lock_fail_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
99 -force 101 && mv 'cal_lock_fail_out/output.${gxy2omsext("mzml")}' '$cal_lock_fail_out'
100 #end if 102 #end if
101 #end if 103 #if "models_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
102 ]]></command> 104 && mv 'quality_control_models/output.${gxy2omsext("csv")}' '$quality_control_models'
105 #end if
106 #if "models_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
107 && mv 'quality_control_models_plot/output.${gxy2omsext("png")}' '$quality_control_models_plot'
108 #end if
109 #if "residuals_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
110 && mv 'quality_control_residuals/output.${gxy2omsext("csv")}' '$quality_control_residuals'
111 #end if
112 #if "residuals_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
113 && mv 'quality_control_residuals_plot/output.${gxy2omsext("png")}' '$quality_control_residuals_plot'
114 #end if
115 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
116 && mv '@EXECUTABLE@.ctd' '$ctd_out'
117 #end if]]></command>
118 <configfiles>
119 <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>
121 </configfiles>
103 <inputs> 122 <inputs>
104 <param name="param_in" type="data" format="mzml" optional="False" label="Input peak file" help="(-in) "/> 123 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input peak file" help=" select mzml data sets(s)"/>
105 <param name="param_rscript_executable" type="data" format="txt" value="Rscript" label="Path to the Rscript executable (default: 'Rscript')" help="(-rscript_executable) "/> 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=""/>
106 <param name="param_ppm_match_tolerance" type="float" value="25.0" label="Finding calibrants in raw data uses this tolerance (for lock masses and ID's)" help="(-ppm_match_tolerance) "/> 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)">
107 <repeat name="rep_param_ms_level" min="0" max="1" title="param_ms_level"> 126 <expand macro="list_integer_valsan"/>
108 <param name="param_ms_level" type="text" size="30" value="1 2 3" label="Target MS levels to apply the transformation onto" help="(-ms_level) Does not affect calibrant collection"> 127 </param>
109 <sanitizer> 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"/>
110 <valid initial="string.printable"> 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">
111 <remove value="'"/> 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)"/>
112 <remove value="&quot;"/> 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)"/>
113 </valid> 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"/>
114 </sanitizer> 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"/>
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="">
135 <option value="linear">linear</option>
136 <option value="linear_weighted" selected="true">linear_weighted</option>
137 <option value="quadratic">quadratic</option>
138 <option value="quadratic_weighted">quadratic_weighted</option>
139 <expand macro="list_string_san"/>
115 </param> 140 </param>
116 </repeat> 141 </section>
117 <param name="param_RT_chunking" type="float" value="300.0" label="RT window (one-sided, i.e" help="(-RT_chunking) 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"/> 142 <section name="RANSAC" title="Robust outlier removal using RANSAC" help="" expanded="false">
118 <param name="param_cal_id_in" type="data" format="idxml,featurexml" optional="True" label="Identifications or features whose peptide ID's serve as calibration masses" help="(-id_in) "/> 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=""/>
119 <param name="param_cal_lock_in" type="data" format="tabular" 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="(-lock_in) "/> 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=""/>
120 <param name="param_cal_lock_require_mono" display="radio" type="boolean" truevalue="-cal:lock_require_mono" falsevalue="" checked="false" optional="True" label="Require all lock masses to be monoisotopic, i.e" help="(-lock_require_mono) not the iso1, iso2 etc ('charge' column is used to determine the spacing). Peaks which are not mono-isotopic are not used"/> 145 <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=""/>
121 <param name="param_cal_lock_require_iso" display="radio" type="boolean" truevalue="-cal:lock_require_iso" falsevalue="" checked="false" optional="True" label="Require all lock masses to have at least the +1 isotope" help="(-lock_require_iso) Peaks without isotope pattern are not used"/> 146 <param name="iter" argument="-RANSAC:iter" type="integer" optional="true" value="70" label="Maximal # iterations" help=""/>
122 <param name="param_cal_model_type" display="radio" type="select" optional="False" value="linear_weighted" label="Type of function to be fitted to the calibration points" help="(-model_type) "> 147 </section>
123 <option value="linear">linear</option> 148 <section name="goodness" title="Thresholds for accepting calibration success" help="" expanded="false">
124 <option value="linear_weighted" selected="true">linear_weighted</option> 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=""/>
125 <option value="quadratic">quadratic</option> 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=""/>
126 <option value="quadratic_weighted">quadratic_weighted</option> 151 </section>
152 <section name="quality_control" title="Tables and plots to verify calibration performance" help="" expanded="false"/>
153 <expand macro="adv_opts_macro">
154 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
155 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
156 <expand macro="list_string_san"/>
157 </param>
158 </expand>
159 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
160 <option value="lock_out_FLAG">lock_out (Plot image of pre- and post calibration errors)</option>
161 <option value="lock_fail_out_FLAG">lock_fail_out (Plot image of pre- and post calibration errors)</option>
162 <option value="models_FLAG">models (Plot image of pre- and post calibration errors)</option>
163 <option value="models_plot_FLAG">models_plot (Plot image of pre- and post calibration errors)</option>
164 <option value="residuals_FLAG">residuals (Plot image of pre- and post calibration errors)</option>
165 <option value="residuals_plot_FLAG">residuals_plot (Plot image of pre- and post calibration errors)</option>
166 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
127 </param> 167 </param>
128 <param name="param_RANSAC_enabled" display="radio" type="boolean" truevalue="-RANSAC:enabled" falsevalue="" checked="false" optional="True" label="Apply RANSAC to calibration points to remove outliers before fitting a model" help="(-enabled) "/>
129 <param name="param_RANSAC_threshold" type="float" value="10.0" label="Threshold for accepting inliers (instrument precision (not accuracy!) as ppm^2 distance)" help="(-threshold) "/>
130 <param name="param_RANSAC_pc_inliers" type="integer" min="1" max="99" optional="True" value="30" label="Minimum percentage (of available data) of inliers (&lt;threshold away from model) to accept the model" help="(-pc_inliers) "/>
131 <param name="param_RANSAC_iter" type="integer" value="70" label="Maximal # iterations" help="(-iter) "/>
132 <param name="param_goodness_median" type="float" value="4.0" label="The median ppm error of calibrated masses must be smaller than this threshold" help="(-median) "/>
133 <param name="param_goodness_MAD" type="float" value="1.0" label="The median absolute deviation of the ppm error of calibrated masses must be smaller than this threshold" help="(-MAD) "/>
134 <expand macro="advanced_options">
135 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
136 </expand>
137 </inputs> 168 </inputs>
138 <outputs> 169 <outputs>
139 <data name="param_out" format="mzml"/> 170 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
140 <data name="param_cal_lock_out" format="mzml"/> 171 <data name="cal_lock_out" label="${tool.name} on ${on_string}: cal:lock_out" format="mzml">
141 <data name="param_cal_lock_fail_out" format="mzml"/> 172 <filter>OPTIONAL_OUTPUTS is not None and "lock_out_FLAG" in OPTIONAL_OUTPUTS</filter>
142 <data name="param_quality_control_models" format="tabular"/> 173 </data>
143 <data name="param_quality_control_models_plot" format="png"/> 174 <data name="cal_lock_fail_out" label="${tool.name} on ${on_string}: cal:lock_fail_out" format="mzml">
144 <data name="param_quality_control_residuals" format="tabular"/> 175 <filter>OPTIONAL_OUTPUTS is not None and "lock_fail_out_FLAG" in OPTIONAL_OUTPUTS</filter>
145 <data name="param_quality_control_residuals_plot" format="png"/> 176 </data>
177 <data name="quality_control_models" label="${tool.name} on ${on_string}: quality_control:models" format="csv">
178 <filter>OPTIONAL_OUTPUTS is not None and "models_FLAG" in OPTIONAL_OUTPUTS</filter>
179 </data>
180 <data name="quality_control_models_plot" label="${tool.name} on ${on_string}: quality_control:models_plot" format="png">
181 <filter>OPTIONAL_OUTPUTS is not None and "models_plot_FLAG" in OPTIONAL_OUTPUTS</filter>
182 </data>
183 <data name="quality_control_residuals" label="${tool.name} on ${on_string}: quality_control:residuals" format="csv">
184 <filter>OPTIONAL_OUTPUTS is not None and "residuals_FLAG" in OPTIONAL_OUTPUTS</filter>
185 </data>
186 <data name="quality_control_residuals_plot" label="${tool.name} on ${on_string}: quality_control:residuals_plot" format="png">
187 <filter>OPTIONAL_OUTPUTS is not None and "residuals_plot_FLAG" in OPTIONAL_OUTPUTS</filter>
188 </data>
189 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
190 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
191 </data>
146 </outputs> 192 </outputs>
147 <help>Applies an internal mass recalibration. 193 <tests>
148 194 <expand macro="autotest_InternalCalibration"/>
149 195 <expand macro="manutest_InternalCalibration"/>
150 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_InternalCalibration.html</help> 196 </tests>
197 <help><![CDATA[Applies an internal mass recalibration.
198
199
200 For more information, visit http://www.openms.de/documentation/TOPP_InternalCalibration.html]]></help>
201 <expand macro="references"/>
151 </tool> 202 </tool>