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comparison OpenSwathChromatogramExtractor.xml @ 13:f78d734b7c01 draft default tip

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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 19:13:34 +0000
parents 71555764c24a
children
comparison
equal deleted inserted replaced
12:50cbdbc12198 13:f78d734b7c01
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: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Extract chromatograms (XIC) from a MS2 map file.</description> 5 <description>Extract chromatograms (XIC) from a MS2 map file.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</token> 7 <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</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@
16 #import re 14 #import re
17 15
18 ## Preprocessing 16 ## Preprocessing
19 mkdir in && 17 mkdir in_cond.in &&
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } 18 #if $in_cond.in_select == "no"
19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
20 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
21 #else
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
23 #end if
21 mkdir tr && 24 mkdir tr &&
22 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && 25 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
23 #if $rt_norm: 26 #if $rt_norm:
24 mkdir rt_norm && 27 mkdir rt_norm &&
25 ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' && 28 ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
31 set -o pipefail && 34 set -o pipefail &&
32 @EXECUTABLE@ -write_ctd ./ && 35 @EXECUTABLE@ -write_ctd ./ &&
33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 36 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 37 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
35 -in 38 -in
36 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} 39 #if $in_cond.in_select == "no"
40 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
41 #else
42 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
43 #end if
37 -tr 44 -tr
38 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' 45 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
39 #if $rt_norm: 46 #if $rt_norm:
40 -rt_norm 47 -rt_norm
41 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' 48 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)'
51 <configfiles> 58 <configfiles>
52 <inputs name="args_json" data_style="paths"/> 59 <inputs name="args_json" data_style="paths"/>
53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 60 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
54 </configfiles> 61 </configfiles>
55 <inputs> 62 <inputs>
56 <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/> 63 <conditional name="in_cond">
57 <param name="tr" argument="-tr" type="data" format="csv,traml" optional="false" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/> 64 <param name="in_select" type="select" label="Run tool in batch mode for -in">
58 <param name="rt_norm" argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help=" select trafoxml data sets(s)"/> 65 <option value="no">No: process all datasets jointly</option>
59 <param name="min_upper_edge_dist" argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help=""/> 66 <option value="yes">Yes: process each dataset in an independent job</option>
60 <param name="rt_window" argument="-rt_window" type="float" optional="true" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range)" help="This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side"/> 67 </param>
61 <param name="ion_mobility_window" argument="-ion_mobility_window" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/> 68 <when value="no">
62 <param name="mz_window" argument="-mz_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag)" help="This is the full window size, e.g. 100 ppm would extract 50 ppm on either side"/> 69 <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/>
63 <param name="ppm" argument="-ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="m/z extraction_window is in ppm" help=""/> 70 </when>
64 <param name="is_swath" argument="-is_swath" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if the data is SWATH data" help=""/> 71 <when value="yes">
65 <param name="extract_MS1" argument="-extract_MS1" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extract the MS1 transitions based on the precursor values in the TraML file (useful for extracting MS1 XIC)" help=""/> 72 <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/>
73 </when>
74 </conditional>
75 <param argument="-tr" type="data" format="csv,traml" optional="false" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
76 <param argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help=" select trafoxml data sets(s)"/>
77 <param argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help=""/>
78 <param argument="-rt_window" type="float" optional="true" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range)" help="This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side"/>
79 <param argument="-ion_mobility_window" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/>
80 <param argument="-mz_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag)" help="This is the full window size, e.g. 100 ppm would extract 50 ppm on either side"/>
81 <param argument="-ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="m/z extraction_window is in ppm" help=""/>
82 <param argument="-is_swath" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if the data is SWATH data" help=""/>
83 <param argument="-extract_MS1" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extract the MS1 transitions based on the precursor values in the TraML file (useful for extracting MS1 XIC)" help=""/>
66 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false"> 84 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
67 <param name="type" argument="-model:type" display="radio" type="select" optional="false" label="Type of model" help=""> 85 <param name="type" argument="-model:type" type="select" optional="true" label="Type of model" help="">
68 <option value="linear" selected="true">linear</option> 86 <option value="linear" selected="true">linear</option>
69 <option value="b_spline">b_spline</option> 87 <option value="b_spline">b_spline</option>
70 <option value="interpolated">interpolated</option> 88 <option value="interpolated">interpolated</option>
71 <option value="lowess">lowess</option> 89 <option value="lowess">lowess</option>
72 <expand macro="list_string_san"/> 90 <expand macro="list_string_san" name="type"/>
73 </param> 91 </param>
74 <param name="symmetric_regression" argument="-model:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/> 92 <param name="symmetric_regression" argument="-model:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
75 </section> 93 </section>
76 <expand macro="adv_opts_macro"> 94 <expand macro="adv_opts_macro">
77 <param name="extraction_function" argument="-extraction_function" display="radio" type="select" optional="false" label="Function used to extract the signal" help=""> 95 <param argument="-extraction_function" type="select" optional="true" label="Function used to extract the signal" help="">
78 <option value="tophat" selected="true">tophat</option> 96 <option value="tophat" selected="true">tophat</option>
79 <option value="bartlett">bartlett</option> 97 <option value="bartlett">bartlett</option>
80 <expand macro="list_string_san"/> 98 <expand macro="list_string_san" name="extraction_function"/>
81 </param> 99 </param>
82 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 100 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
83 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 101 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
84 <expand macro="list_string_san"/> 102 <expand macro="list_string_san" name="test"/>
85 </param> 103 </param>
86 </expand> 104 </expand>
87 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 105 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
88 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 106 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
89 </param> 107 </param>
92 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 110 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
93 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 111 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
94 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 112 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
95 </data> 113 </data>
96 </outputs> 114 </outputs>
97 <tests> 115 <tests><!-- TOPP_OpenSwathChromatogramExtractor_test_1 -->
98 <expand macro="autotest_OpenSwathChromatogramExtractor"/> 116 <test expect_num_outputs="2">
99 <expand macro="manutest_OpenSwathChromatogramExtractor"/> 117 <section name="adv_opts">
118 <param name="extraction_function" value="tophat"/>
119 <param name="force" value="false"/>
120 <param name="test" value="true"/>
121 </section>
122 <conditional name="in_cond">
123 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
124 </conditional>
125 <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
126 <output name="out" file="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
127 <param name="min_upper_edge_dist" value="0.0"/>
128 <param name="rt_window" value="-1.0"/>
129 <param name="ion_mobility_window" value="-1.0"/>
130 <param name="mz_window" value="0.05"/>
131 <param name="ppm" value="false"/>
132 <param name="is_swath" value="false"/>
133 <param name="extract_MS1" value="false"/>
134 <section name="model">
135 <param name="type" value="linear"/>
136 <param name="symmetric_regression" value="false"/>
137 </section>
138 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
139 <output name="ctd_out" ftype="xml">
140 <assert_contents>
141 <is_valid_xml/>
142 </assert_contents>
143 </output>
144 </test>
145 <!-- TOPP_OpenSwathChromatogramExtractor_test_2 -->
146 <test expect_num_outputs="2">
147 <section name="adv_opts">
148 <param name="extraction_function" value="tophat"/>
149 <param name="force" value="false"/>
150 <param name="test" value="true"/>
151 </section>
152 <conditional name="in_cond">
153 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
154 </conditional>
155 <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
156 <param name="rt_norm" value="OpenSwathChromatogramExtractor_input.trafoXML"/>
157 <output name="out" file="OpenSwathChromatogramExtractor_output_2.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
158 <param name="min_upper_edge_dist" value="0.0"/>
159 <param name="rt_window" value="50.0"/>
160 <param name="ion_mobility_window" value="-1.0"/>
161 <param name="mz_window" value="0.05"/>
162 <param name="ppm" value="false"/>
163 <param name="is_swath" value="false"/>
164 <param name="extract_MS1" value="false"/>
165 <section name="model">
166 <param name="type" value="linear"/>
167 <param name="symmetric_regression" value="false"/>
168 </section>
169 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
170 <output name="ctd_out" ftype="xml">
171 <assert_contents>
172 <is_valid_xml/>
173 </assert_contents>
174 </output>
175 </test>
176 <!-- TOPP_OpenSwathChromatogramExtractor_test_3 -->
177 <test expect_num_outputs="2">
178 <section name="adv_opts">
179 <param name="extraction_function" value="tophat"/>
180 <param name="force" value="false"/>
181 <param name="test" value="true"/>
182 </section>
183 <conditional name="in_cond">
184 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
185 </conditional>
186 <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
187 <output name="out" file="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
188 <param name="min_upper_edge_dist" value="0.0"/>
189 <param name="rt_window" value="-1.0"/>
190 <param name="ion_mobility_window" value="-1.0"/>
191 <param name="mz_window" value="0.05"/>
192 <param name="ppm" value="false"/>
193 <param name="is_swath" value="false"/>
194 <param name="extract_MS1" value="true"/>
195 <section name="model">
196 <param name="type" value="linear"/>
197 <param name="symmetric_regression" value="false"/>
198 </section>
199 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
200 <output name="ctd_out" ftype="xml">
201 <assert_contents>
202 <is_valid_xml/>
203 </assert_contents>
204 </output>
205 </test>
206 <!-- TOPP_OpenSwathChromatogramExtractor_test_4 -->
207 <test expect_num_outputs="2">
208 <section name="adv_opts">
209 <param name="extraction_function" value="tophat"/>
210 <param name="force" value="false"/>
211 <param name="test" value="true"/>
212 </section>
213 <conditional name="in_cond">
214 <param name="in" value="OpenSwathChromatogramExtractor_4_input.mzML"/>
215 </conditional>
216 <param name="tr" value="OpenSwathChromatogramExtractor_4_input.TraML"/>
217 <output name="out" file="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
218 <param name="min_upper_edge_dist" value="0.0"/>
219 <param name="rt_window" value="-1.0"/>
220 <param name="ion_mobility_window" value="0.05"/>
221 <param name="mz_window" value="0.05"/>
222 <param name="ppm" value="false"/>
223 <param name="is_swath" value="true"/>
224 <param name="extract_MS1" value="false"/>
225 <section name="model">
226 <param name="type" value="linear"/>
227 <param name="symmetric_regression" value="false"/>
228 </section>
229 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
230 <output name="ctd_out" ftype="xml">
231 <assert_contents>
232 <is_valid_xml/>
233 </assert_contents>
234 </output>
235 </test>
236 <!-- TOPP_OpenSwathChromatogramExtractor_test_5 -->
237 <test expect_num_outputs="2">
238 <section name="adv_opts">
239 <param name="extraction_function" value="tophat"/>
240 <param name="force" value="false"/>
241 <param name="test" value="true"/>
242 </section>
243 <conditional name="in_cond">
244 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
245 </conditional>
246 <param name="tr" value="OpenSwathChromatogramExtractor_5_input.TraML"/>
247 <output name="out" file="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
248 <param name="min_upper_edge_dist" value="0.0"/>
249 <param name="rt_window" value="-1.0"/>
250 <param name="ion_mobility_window" value="-1.0"/>
251 <param name="mz_window" value="0.05"/>
252 <param name="ppm" value="false"/>
253 <param name="is_swath" value="false"/>
254 <param name="extract_MS1" value="true"/>
255 <section name="model">
256 <param name="type" value="linear"/>
257 <param name="symmetric_regression" value="false"/>
258 </section>
259 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
260 <output name="ctd_out" ftype="xml">
261 <assert_contents>
262 <is_valid_xml/>
263 </assert_contents>
264 </output>
265 </test>
100 </tests> 266 </tests>
101 <help><![CDATA[Extract chromatograms (XIC) from a MS2 map file. 267 <help><![CDATA[Extract chromatograms (XIC) from a MS2 map file.
102 268
103 269
104 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathChromatogramExtractor.html]]></help> 270 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathChromatogramExtractor.html]]></help>
105 <expand macro="references"/> 271 <expand macro="references"/>
106 </tool> 272 </tool>