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comparison OpenSwathDecoyGenerator.xml @ 13:496cf619e311 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 19:18:22 +0000
parents 3769d3a7e9ba
children e833a89f25c8
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12:f861ec9fbe59 13:496cf619e311
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="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <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> 5 <description>Generates decoys according to different models for a specific TraML</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</token> 7 <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</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@
39 <configfiles> 37 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 38 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 40 </configfiles>
43 <inputs> 41 <inputs>
44 <param name="in" argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/> 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)"/>
45 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help=""> 43 <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
46 <option value="TraML">traml</option> 44 <option value="TraML">traml</option>
47 <option value="pqp">pqp</option> 45 <option value="pqp">pqp</option>
48 <option value="tsv">tabular (tsv)</option> 46 <option value="tsv">tabular (tsv)</option>
49 <expand macro="list_string_san"/> 47 <expand macro="list_string_san" name="out_type"/>
50 </param> 48 </param>
51 <param name="method" argument="-method" display="radio" type="select" optional="false" label="Decoy generation method" help=""> 49 <param argument="-method" type="select" optional="true" label="Decoy generation method" help="">
52 <option value="shuffle" selected="true">shuffle</option> 50 <option value="shuffle" selected="true">shuffle</option>
53 <option value="pseudo-reverse">pseudo-reverse</option> 51 <option value="pseudo-reverse">pseudo-reverse</option>
54 <option value="reverse">reverse</option> 52 <option value="reverse">reverse</option>
55 <option value="shift">shift</option> 53 <option value="shift">shift</option>
56 <expand macro="list_string_san"/> 54 <expand macro="list_string_san" name="method"/>
57 </param> 55 </param>
58 <param name="decoy_tag" argument="-decoy_tag" type="text" optional="true" value="DECOY_" label="decoy tag" help=""> 56 <param argument="-decoy_tag" type="text" optional="true" value="DECOY_" label="decoy tag" help="">
59 <expand macro="list_string_san"/> 57 <expand macro="list_string_san" name="decoy_tag"/>
60 </param> 58 </param>
61 <param name="switchKR" 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=""/>
62 <expand macro="adv_opts_macro"> 60 <expand macro="adv_opts_macro">
63 <param name="min_decoy_fraction" 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" optional="true" value="0.8" label="Minimum fraction of decoy / target peptides and proteins" help=""/>
64 <param name="aim_decoy_fraction" 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" 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=""/>
65 <param name="shuffle_max_attempts" 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" optional="true" value="30" label="shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm" help=""/>
66 <param name="shuffle_sequence_identity_threshold" 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" optional="true" value="0.5" label="shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm" help=""/>
67 <param name="shift_precursor_mz_shift" 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" optional="true" value="0.0" label="shift: precursor ion MZ shift in Thomson for shift decoy method" help=""/>
68 <param name="shift_product_mz_shift" 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" optional="true" value="20.0" label="shift: fragment ion MZ shift in Thomson for shift decoy method" help=""/>
69 <param name="product_mz_threshold" 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" optional="true" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/>
70 <param name="allowed_fragment_types" argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help=""> 68 <param argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help="">
71 <expand macro="list_string_san"/> 69 <expand macro="list_string_san" name="allowed_fragment_types"/>
72 </param> 70 </param>
73 <param name="allowed_fragment_charges" 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" optional="true" value="1,2,3,4" label="allowed fragment charge states" help="">
74 <expand macro="list_string_san"/> 72 <expand macro="list_string_san" name="allowed_fragment_charges"/>
75 </param> 73 </param>
76 <param name="enable_detection_specific_losses" 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=""/>
77 <param name="enable_detection_unspecific_losses" 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=""/>
78 <param name="separate" 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=""/>
79 <param name="force" 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=""/>
80 <param name="test" 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" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
81 <expand macro="list_string_san"/> 79 <expand macro="list_string_san" name="test"/>
82 </param> 80 </param>
83 </expand> 81 </expand>
84 <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">
85 <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>
86 </param> 84 </param>
87 </inputs> 85 </inputs>
88 <outputs> 86 <outputs>
89 <data name="out" label="${tool.name} on ${on_string}: out"> 87 <data name="out" label="${tool.name} on ${on_string}: out" format="traml">
90 <change_format> 88 <change_format>
91 <when input="out_type" value="TraML" format="traml"/>
92 <when input="out_type" value="pqp" format="pqp"/> 89 <when input="out_type" value="pqp" format="pqp"/>
93 <when input="out_type" value="tsv" format="tabular"/> 90 <when input="out_type" value="tsv" format="tabular"/>
94 </change_format> 91 </change_format>
95 </data> 92 </data>
96 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 93 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
97 <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>
98 </data> 95 </data>
99 </outputs> 96 </outputs>
100 <tests> 97 <tests><!-- TOPP_OpenSwathDecoyGenerator_test_1 -->
101 <expand macro="autotest_OpenSwathDecoyGenerator"/> 98 <test expect_num_outputs="2">
102 <expand macro="manutest_OpenSwathDecoyGenerator"/> 99 <section name="adv_opts">
100 <param name="min_decoy_fraction" value="0.8"/>
101 <param name="aim_decoy_fraction" value="1.0"/>
102 <param name="shuffle_max_attempts" value="30"/>
103 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
104 <param name="shift_precursor_mz_shift" value="0.0"/>
105 <param name="shift_product_mz_shift" value="20.0"/>
106 <param name="product_mz_threshold" value="0.025"/>
107 <param name="allowed_fragment_types" value="b,y"/>
108 <param name="allowed_fragment_charges" value="1,2,3,4"/>
109 <param name="enable_detection_specific_losses" value="false"/>
110 <param name="enable_detection_unspecific_losses" value="false"/>
111 <param name="separate" value="true"/>
112 <param name="force" value="false"/>
113 <param name="test" value="true"/>
114 </section>
115 <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 <param name="out_type" value="TraML"/>
118 <param name="method" value="pseudo-reverse"/>
119 <param name="decoy_tag" value="DECOY_"/>
120 <param name="switchKR" value="false"/>
121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
122 <output name="ctd_out" ftype="xml">
123 <assert_contents>
124 <is_valid_xml/>
125 </assert_contents>
126 </output>
127 </test>
128 <!-- TOPP_OpenSwathDecoyGenerator_test_2 -->
129 <test expect_num_outputs="2">
130 <section name="adv_opts">
131 <param name="min_decoy_fraction" value="0.8"/>
132 <param name="aim_decoy_fraction" value="1.0"/>
133 <param name="shuffle_max_attempts" value="30"/>
134 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
135 <param name="shift_precursor_mz_shift" value="0.0"/>
136 <param name="shift_product_mz_shift" value="20.0"/>
137 <param name="product_mz_threshold" value="0.8"/>
138 <param name="allowed_fragment_types" value="b,y"/>
139 <param name="allowed_fragment_charges" value="1,2,3,4"/>
140 <param name="enable_detection_specific_losses" value="false"/>
141 <param name="enable_detection_unspecific_losses" value="false"/>
142 <param name="separate" value="false"/>
143 <param name="force" value="false"/>
144 <param name="test" value="true"/>
145 </section>
146 <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"/>
148 <param name="out_type" value="TraML"/>
149 <param name="method" value="pseudo-reverse"/>
150 <param name="decoy_tag" value="DECOY_"/>
151 <param name="switchKR" value="false"/>
152 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
153 <output name="ctd_out" ftype="xml">
154 <assert_contents>
155 <is_valid_xml/>
156 </assert_contents>
157 </output>
158 </test>
159 <!-- TOPP_OpenSwathDecoyGenerator_test_3 -->
160 <test expect_num_outputs="2">
161 <section name="adv_opts">
162 <param name="min_decoy_fraction" value="0.8"/>
163 <param name="aim_decoy_fraction" value="1.0"/>
164 <param name="shuffle_max_attempts" value="30"/>
165 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
166 <param name="shift_precursor_mz_shift" value="0.0"/>
167 <param name="shift_product_mz_shift" value="20.0"/>
168 <param name="product_mz_threshold" value="0.025"/>
169 <param name="allowed_fragment_types" value="b,y"/>
170 <param name="allowed_fragment_charges" value="1,2,3,4"/>
171 <param name="enable_detection_specific_losses" value="false"/>
172 <param name="enable_detection_unspecific_losses" value="false"/>
173 <param name="separate" value="true"/>
174 <param name="force" value="false"/>
175 <param name="test" value="true"/>
176 </section>
177 <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"/>
179 <param name="out_type" value="TraML"/>
180 <param name="method" value="pseudo-reverse"/>
181 <param name="decoy_tag" value="DECOY_"/>
182 <param name="switchKR" value="false"/>
183 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
184 <output name="ctd_out" ftype="xml">
185 <assert_contents>
186 <is_valid_xml/>
187 </assert_contents>
188 </output>
189 </test>
190 <!-- TOPP_OpenSwathDecoyGenerator_test_4 -->
191 <test expect_num_outputs="2">
192 <section name="adv_opts">
193 <param name="min_decoy_fraction" value="0.4"/>
194 <param name="aim_decoy_fraction" value="1.0"/>
195 <param name="shuffle_max_attempts" value="30"/>
196 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
197 <param name="shift_precursor_mz_shift" value="0.0"/>
198 <param name="shift_product_mz_shift" value="20.0"/>
199 <param name="product_mz_threshold" value="0.025"/>
200 <param name="allowed_fragment_types" value="b,y"/>
201 <param name="allowed_fragment_charges" value="1,2,3,4"/>
202 <param name="enable_detection_specific_losses" value="true"/>
203 <param name="enable_detection_unspecific_losses" value="true"/>
204 <param name="separate" value="true"/>
205 <param name="force" value="false"/>
206 <param name="test" value="true"/>
207 </section>
208 <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"/>
210 <param name="out_type" value="TraML"/>
211 <param name="method" value="pseudo-reverse"/>
212 <param name="decoy_tag" value="DECOY_"/>
213 <param name="switchKR" value="true"/>
214 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
215 <output name="ctd_out" ftype="xml">
216 <assert_contents>
217 <is_valid_xml/>
218 </assert_contents>
219 </output>
220 </test>
103 </tests> 221 </tests>
104 <help><![CDATA[Generates decoys according to different models for a specific TraML 222 <help><![CDATA[Generates decoys according to different models for a specific TraML
105 223
106 224
107 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathDecoyGenerator.html]]></help> 225 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathDecoyGenerator.html]]></help>
108 <expand macro="references"/> 226 <expand macro="references"/>
109 </tool> 227 </tool>