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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 21:45:00 +0000
parents 496cf619e311
children
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13:496cf619e311 14:e833a89f25c8
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: [Targeted Experiments]--> 2 <!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
4 <tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Generates decoys according to different models for a specific TraML</description> 4 <description>Generates decoys according to different models for a specific TraML</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</token> 6 <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
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 19
21 ## Main program call 20 ## Main program call
22 21
23 set -o pipefail && 22 set -o pipefail &&
37 <configfiles> 36 <configfiles>
38 <inputs name="args_json" data_style="paths"/> 37 <inputs name="args_json" data_style="paths"/>
39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
40 </configfiles> 39 </configfiles>
41 <inputs> 40 <inputs>
42 <param argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/> 41 <param argument="-in" type="data" format="mrm,pqp,tabular,traml" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/>
43 <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help=""> 42 <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
44 <option value="TraML">traml</option> 43 <option value="TraML">traml</option>
45 <option value="pqp">pqp</option> 44 <option value="pqp">pqp</option>
46 <option value="tsv">tabular (tsv)</option> 45 <option value="tsv">tabular (tsv)</option>
46 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
47 <expand macro="list_string_san" name="out_type"/> 47 <expand macro="list_string_san" name="out_type"/>
48 </param> 48 </param>
49 <param argument="-method" type="select" optional="true" label="Decoy generation method" help=""> 49 <param argument="-method" type="select" label="Decoy generation method" help="">
50 <option value="shuffle" selected="true">shuffle</option> 50 <option value="shuffle" selected="true">shuffle</option>
51 <option value="pseudo-reverse">pseudo-reverse</option> 51 <option value="pseudo-reverse">pseudo-reverse</option>
52 <option value="reverse">reverse</option> 52 <option value="reverse">reverse</option>
53 <option value="shift">shift</option> 53 <option value="shift">shift</option>
54 <expand macro="list_string_san" name="method"/> 54 <expand macro="list_string_san" name="method"/>
55 </param> 55 </param>
56 <param argument="-decoy_tag" type="text" optional="true" value="DECOY_" label="decoy tag" help=""> 56 <param argument="-decoy_tag" type="text" value="DECOY_" label="decoy tag" help="">
57 <expand macro="list_string_san" name="decoy_tag"/> 57 <expand macro="list_string_san" name="decoy_tag"/>
58 </param> 58 </param>
59 <param argument="-switchKR" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to switch terminal K and R (to achieve different precursor mass)" help=""/> 59 <param argument="-switchKR" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to switch terminal K and R (to achieve different precursor mass)" help=""/>
60 <expand macro="adv_opts_macro"> 60 <expand macro="adv_opts_macro">
61 <param argument="-min_decoy_fraction" type="float" optional="true" value="0.8" label="Minimum fraction of decoy / target peptides and proteins" help=""/> 61 <param argument="-min_decoy_fraction" type="float" value="0.8" label="Minimum fraction of decoy / target peptides and proteins" help=""/>
62 <param argument="-aim_decoy_fraction" type="float" optional="true" value="1.0" label="Number of decoys the algorithm should generate (if unequal to 1, the algorithm will randomly select N peptides for decoy generation)" help=""/> 62 <param argument="-aim_decoy_fraction" type="float" value="1.0" label="Number of decoys the algorithm should generate (if unequal to 1, the algorithm will randomly select N peptides for decoy generation)" help=""/>
63 <param argument="-shuffle_max_attempts" type="integer" optional="true" value="30" label="shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm" help=""/> 63 <param argument="-shuffle_max_attempts" type="integer" value="30" label="shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm" help=""/>
64 <param argument="-shuffle_sequence_identity_threshold" type="float" optional="true" value="0.5" label="shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm" help=""/> 64 <param argument="-shuffle_sequence_identity_threshold" type="float" value="0.5" label="shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm" help=""/>
65 <param argument="-shift_precursor_mz_shift" type="float" optional="true" value="0.0" label="shift: precursor ion MZ shift in Thomson for shift decoy method" help=""/> 65 <param argument="-shift_precursor_mz_shift" type="float" value="0.0" label="shift: precursor ion MZ shift in Thomson for shift decoy method" help=""/>
66 <param argument="-shift_product_mz_shift" type="float" optional="true" value="20.0" label="shift: fragment ion MZ shift in Thomson for shift decoy method" help=""/> 66 <param argument="-shift_product_mz_shift" type="float" value="20.0" label="shift: fragment ion MZ shift in Thomson for shift decoy method" help=""/>
67 <param argument="-product_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/> 67 <param argument="-product_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/>
68 <param argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help=""> 68 <param argument="-allowed_fragment_types" type="text" value="b,y" label="allowed fragment types" help="">
69 <expand macro="list_string_san" name="allowed_fragment_types"/> 69 <expand macro="list_string_san" name="allowed_fragment_types"/>
70 </param> 70 </param>
71 <param argument="-allowed_fragment_charges" type="text" optional="true" value="1,2,3,4" label="allowed fragment charge states" help=""> 71 <param argument="-allowed_fragment_charges" type="text" value="1,2,3,4" label="allowed fragment charge states" help="">
72 <expand macro="list_string_san" name="allowed_fragment_charges"/> 72 <expand macro="list_string_san" name="allowed_fragment_charges"/>
73 </param> 73 </param>
74 <param argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/> 74 <param argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/>
75 <param argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/> 75 <param argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/>
76 <param argument="-separate" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if decoys should not be appended to targets" help=""/> 76 <param argument="-separate" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if decoys should not be appended to targets" help=""/>
77 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 77 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
78 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 78 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
79 <expand macro="list_string_san" name="test"/> 79 <expand macro="list_string_san" name="test"/>
80 </param> 80 </param>
81 </expand> 81 </expand>
82 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 82 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
83 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 83 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
92 </data> 92 </data>
93 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 93 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
94 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 94 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
95 </data> 95 </data>
96 </outputs> 96 </outputs>
97 <tests><!-- TOPP_OpenSwathDecoyGenerator_test_1 --> 97 <tests>
98 <!-- TOPP_OpenSwathDecoyGenerator_test_1 -->
98 <test expect_num_outputs="2"> 99 <test expect_num_outputs="2">
99 <section name="adv_opts"> 100 <section name="adv_opts">
100 <param name="min_decoy_fraction" value="0.8"/> 101 <param name="min_decoy_fraction" value="0.8"/>
101 <param name="aim_decoy_fraction" value="1.0"/> 102 <param name="aim_decoy_fraction" value="1.0"/>
102 <param name="shuffle_max_attempts" value="30"/> 103 <param name="shuffle_max_attempts" value="30"/>
111 <param name="separate" value="true"/> 112 <param name="separate" value="true"/>
112 <param name="force" value="false"/> 113 <param name="force" value="false"/>
113 <param name="test" value="true"/> 114 <param name="test" value="true"/>
114 </section> 115 </section>
115 <param name="in" value="OpenSwathDecoyGenerator_input.TraML"/> 116 <param name="in" value="OpenSwathDecoyGenerator_input.TraML"/>
116 <output name="out" file="OpenSwathDecoyGenerator_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 117 <output name="out" value="OpenSwathDecoyGenerator_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
117 <param name="out_type" value="TraML"/> 118 <param name="out_type" value="TraML"/>
118 <param name="method" value="pseudo-reverse"/> 119 <param name="method" value="pseudo-reverse"/>
119 <param name="decoy_tag" value="DECOY_"/> 120 <param name="decoy_tag" value="DECOY_"/>
120 <param name="switchKR" value="false"/> 121 <param name="switchKR" value="false"/>
121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 122 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
122 <output name="ctd_out" ftype="xml"> 123 <output name="ctd_out" ftype="xml">
123 <assert_contents> 124 <assert_contents>
124 <is_valid_xml/> 125 <is_valid_xml/>
125 </assert_contents> 126 </assert_contents>
126 </output> 127 </output>
128 <assert_stdout>
129 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
130 </assert_stdout>
127 </test> 131 </test>
128 <!-- TOPP_OpenSwathDecoyGenerator_test_2 --> 132 <!-- TOPP_OpenSwathDecoyGenerator_test_2 -->
129 <test expect_num_outputs="2"> 133 <test expect_num_outputs="2">
130 <section name="adv_opts"> 134 <section name="adv_opts">
131 <param name="min_decoy_fraction" value="0.8"/> 135 <param name="min_decoy_fraction" value="0.8"/>
142 <param name="separate" value="false"/> 146 <param name="separate" value="false"/>
143 <param name="force" value="false"/> 147 <param name="force" value="false"/>
144 <param name="test" value="true"/> 148 <param name="test" value="true"/>
145 </section> 149 </section>
146 <param name="in" value="OpenSwathDecoyGenerator_input_2.TraML"/> 150 <param name="in" value="OpenSwathDecoyGenerator_input_2.TraML"/>
147 <output name="out" file="OpenSwathDecoyGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 151 <output name="out" value="OpenSwathDecoyGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
148 <param name="out_type" value="TraML"/> 152 <param name="out_type" value="TraML"/>
149 <param name="method" value="pseudo-reverse"/> 153 <param name="method" value="pseudo-reverse"/>
150 <param name="decoy_tag" value="DECOY_"/> 154 <param name="decoy_tag" value="DECOY_"/>
151 <param name="switchKR" value="false"/> 155 <param name="switchKR" value="false"/>
152 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 156 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
153 <output name="ctd_out" ftype="xml"> 157 <output name="ctd_out" ftype="xml">
154 <assert_contents> 158 <assert_contents>
155 <is_valid_xml/> 159 <is_valid_xml/>
156 </assert_contents> 160 </assert_contents>
157 </output> 161 </output>
162 <assert_stdout>
163 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
164 </assert_stdout>
158 </test> 165 </test>
159 <!-- TOPP_OpenSwathDecoyGenerator_test_3 --> 166 <!-- TOPP_OpenSwathDecoyGenerator_test_3 -->
160 <test expect_num_outputs="2"> 167 <test expect_num_outputs="2">
161 <section name="adv_opts"> 168 <section name="adv_opts">
162 <param name="min_decoy_fraction" value="0.8"/> 169 <param name="min_decoy_fraction" value="0.8"/>
173 <param name="separate" value="true"/> 180 <param name="separate" value="true"/>
174 <param name="force" value="false"/> 181 <param name="force" value="false"/>
175 <param name="test" value="true"/> 182 <param name="test" value="true"/>
176 </section> 183 </section>
177 <param name="in" value="OpenSwathDecoyGenerator_input_3.TraML"/> 184 <param name="in" value="OpenSwathDecoyGenerator_input_3.TraML"/>
178 <output name="out" file="OpenSwathDecoyGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 185 <output name="out" value="OpenSwathDecoyGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
179 <param name="out_type" value="TraML"/> 186 <param name="out_type" value="TraML"/>
180 <param name="method" value="pseudo-reverse"/> 187 <param name="method" value="pseudo-reverse"/>
181 <param name="decoy_tag" value="DECOY_"/> 188 <param name="decoy_tag" value="DECOY_"/>
182 <param name="switchKR" value="false"/> 189 <param name="switchKR" value="false"/>
183 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 190 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
184 <output name="ctd_out" ftype="xml"> 191 <output name="ctd_out" ftype="xml">
185 <assert_contents> 192 <assert_contents>
186 <is_valid_xml/> 193 <is_valid_xml/>
187 </assert_contents> 194 </assert_contents>
188 </output> 195 </output>
196 <assert_stdout>
197 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
198 </assert_stdout>
189 </test> 199 </test>
190 <!-- TOPP_OpenSwathDecoyGenerator_test_4 --> 200 <!-- TOPP_OpenSwathDecoyGenerator_test_4 -->
191 <test expect_num_outputs="2"> 201 <test expect_num_outputs="2">
192 <section name="adv_opts"> 202 <section name="adv_opts">
193 <param name="min_decoy_fraction" value="0.4"/> 203 <param name="min_decoy_fraction" value="0.4"/>
204 <param name="separate" value="true"/> 214 <param name="separate" value="true"/>
205 <param name="force" value="false"/> 215 <param name="force" value="false"/>
206 <param name="test" value="true"/> 216 <param name="test" value="true"/>
207 </section> 217 </section>
208 <param name="in" value="OpenSwathDecoyGenerator_input_4.tsv" ftype="tabular"/> 218 <param name="in" value="OpenSwathDecoyGenerator_input_4.tsv" ftype="tabular"/>
209 <output name="out" file="OpenSwathDecoyGenerator_output_4.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 219 <output name="out" value="OpenSwathDecoyGenerator_output_4.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
210 <param name="out_type" value="TraML"/> 220 <param name="out_type" value="TraML"/>
211 <param name="method" value="pseudo-reverse"/> 221 <param name="method" value="pseudo-reverse"/>
212 <param name="decoy_tag" value="DECOY_"/> 222 <param name="decoy_tag" value="DECOY_"/>
213 <param name="switchKR" value="true"/> 223 <param name="switchKR" value="true"/>
214 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 224 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
215 <output name="ctd_out" ftype="xml"> 225 <output name="ctd_out" ftype="xml">
216 <assert_contents> 226 <assert_contents>
217 <is_valid_xml/> 227 <is_valid_xml/>
218 </assert_contents> 228 </assert_contents>
219 </output> 229 </output>
230 <assert_stdout>
231 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
232 </assert_stdout>
233 </test>
234 <!-- TOPP_OpenSwathDecoyGenerator_test_5 -->
235 <test expect_num_outputs="2">
236 <section name="adv_opts">
237 <param name="min_decoy_fraction" value="0.4"/>
238 <param name="aim_decoy_fraction" value="1.0"/>
239 <param name="shuffle_max_attempts" value="30"/>
240 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
241 <param name="shift_precursor_mz_shift" value="0.0"/>
242 <param name="shift_product_mz_shift" value="20.0"/>
243 <param name="product_mz_threshold" value="0.025"/>
244 <param name="allowed_fragment_types" value="b,y"/>
245 <param name="allowed_fragment_charges" value="1,2,3,4"/>
246 <param name="enable_detection_specific_losses" value="false"/>
247 <param name="enable_detection_unspecific_losses" value="false"/>
248 <param name="separate" value="false"/>
249 <param name="force" value="false"/>
250 <param name="test" value="true"/>
251 </section>
252 <param name="in" value="OpenSwathDecoyGenerator_input_5.tsv" ftype="tabular"/>
253 <output name="out" value="OpenSwathDecoyGenerator_output_5.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
254 <param name="out_type" value="TraML"/>
255 <param name="method" value="pseudo-reverse"/>
256 <param name="decoy_tag" value="DECOY_"/>
257 <param name="switchKR" value="false"/>
258 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
259 <output name="ctd_out" ftype="xml">
260 <assert_contents>
261 <is_valid_xml/>
262 </assert_contents>
263 </output>
264 <assert_stdout>
265 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
266 </assert_stdout>
220 </test> 267 </test>
221 </tests> 268 </tests>
222 <help><![CDATA[Generates decoys according to different models for a specific TraML 269 <help><![CDATA[Generates decoys according to different models for a specific TraML
223 270
224 271
225 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathDecoyGenerator.html]]></help> 272 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathDecoyGenerator.html]]></help>
226 <expand macro="references"/> 273 <expand macro="references"/>
227 </tool> 274 </tool>