Mercurial > repos > galaxyp > openms_openswathassaygenerator

comparison OpenSwathAssayGenerator.xml @ 13:de7a553552a6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:07:50 +0000
parents a41cd777ced9
children 74d39f98b0c4
comparison
equal deleted inserted replaced
12:2a9ff56cb279 13:de7a553552a6
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="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Generates assays according to different models for a specific TraML</description> 5 <description>Generates assays according to different models for a specific TraML</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathAssayGenerator</token> 7 <token name="@EXECUTABLE@">OpenSwathAssayGenerator</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@
55 <configfiles> 53 <configfiles>
56 <inputs name="args_json" data_style="paths"/> 54 <inputs name="args_json" data_style="paths"/>
57 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 55 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
58 </configfiles> 56 </configfiles>
59 <inputs> 57 <inputs>
60 <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)"/> 58 <param argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/>
61 <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=""> 59 <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
62 <option value="TraML">traml</option> 60 <option value="TraML">traml</option>
63 <option value="pqp">pqp</option> 61 <option value="pqp">pqp</option>
64 <option value="tsv">tabular (tsv)</option> 62 <option value="tsv">tabular (tsv)</option>
65 <expand macro="list_string_san"/> 63 <expand macro="list_string_san" name="out_type"/>
66 </param> 64 </param>
67 <param name="min_transitions" argument="-min_transitions" type="integer" optional="true" value="6" label="minimal number of transitions" help=""/> 65 <param argument="-min_transitions" type="integer" optional="true" value="6" label="minimal number of transitions" help=""/>
68 <param name="max_transitions" argument="-max_transitions" type="integer" optional="true" value="6" label="maximal number of transitions" help=""/> 66 <param argument="-max_transitions" type="integer" optional="true" value="6" label="maximal number of transitions" help=""/>
69 <param name="allowed_fragment_types" argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help=""> 67 <param argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help="">
70 <expand macro="list_string_san"/> 68 <expand macro="list_string_san" name="allowed_fragment_types"/>
71 </param> 69 </param>
72 <param name="allowed_fragment_charges" argument="-allowed_fragment_charges" type="text" optional="true" value="1,2,3,4" label="allowed fragment charge states" help=""> 70 <param argument="-allowed_fragment_charges" type="text" optional="true" value="1,2,3,4" label="allowed fragment charge states" help="">
73 <expand macro="list_string_san"/> 71 <expand macro="list_string_san" name="allowed_fragment_charges"/>
74 </param> 72 </param>
75 <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=""/> 73 <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=""/>
76 <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=""/> 74 <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=""/>
77 <param name="precursor_mz_threshold" argument="-precursor_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help=""/> 75 <param argument="-precursor_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help=""/>
78 <param name="precursor_lower_mz_limit" argument="-precursor_lower_mz_limit" type="float" optional="true" value="400.0" label="lower MZ limit for precursor ions" help=""/> 76 <param argument="-precursor_lower_mz_limit" type="float" optional="true" value="400.0" label="lower MZ limit for precursor ions" help=""/>
79 <param name="precursor_upper_mz_limit" argument="-precursor_upper_mz_limit" type="float" optional="true" value="1200.0" label="upper MZ limit for precursor ions" help=""/> 77 <param argument="-precursor_upper_mz_limit" type="float" optional="true" value="1200.0" label="upper MZ limit for precursor ions" help=""/>
80 <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=""/> 78 <param argument="-product_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/>
81 <param name="product_lower_mz_limit" argument="-product_lower_mz_limit" type="float" optional="true" value="350.0" label="lower MZ limit for fragment ions" help=""/> 79 <param argument="-product_lower_mz_limit" type="float" optional="true" value="350.0" label="lower MZ limit for fragment ions" help=""/>
82 <param name="product_upper_mz_limit" argument="-product_upper_mz_limit" type="float" optional="true" value="2000.0" label="upper MZ limit for fragment ions" help=""/> 80 <param argument="-product_upper_mz_limit" type="float" optional="true" value="2000.0" label="upper MZ limit for fragment ions" help=""/>
83 <param name="swath_windows_file" argument="-swath_windows_file" type="data" format="txt" optional="true" label="Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline" help="Note that the first line is a header and will be skipped select txt data sets(s)"/> 81 <param argument="-swath_windows_file" type="data" format="txt" optional="true" label="Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline" help="Note that the first line is a header and will be skipped select txt data sets(s)"/>
84 <param name="unimod_file" argument="-unimod_file" type="data" format="xml" optional="true" label="(Modified) Unimod XML file (http://www.unimod.org/xml/unimod.xml) describing residue modifiability" help=" select xml data sets(s)"/> 82 <param argument="-unimod_file" type="data" format="xml" optional="true" label="(Modified) Unimod XML file (http://www.unimod.org/xml/unimod.xml) describing residue modifiability" help=" select xml data sets(s)"/>
85 <param name="enable_ipf" argument="-enable_ipf" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions should be generated for IPF" help="Note: Requires setting 'unimod_file'"/> 83 <param argument="-enable_ipf" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions should be generated for IPF" help="Note: Requires setting 'unimod_file'"/>
86 <expand macro="adv_opts_macro"> 84 <expand macro="adv_opts_macro">
87 <param name="max_num_alternative_localizations" argument="-max_num_alternative_localizations" type="integer" optional="true" value="10000" label="IPF: maximum number of site-localization permutations" help=""/> 85 <param argument="-max_num_alternative_localizations" type="integer" optional="true" value="10000" label="IPF: maximum number of site-localization permutations" help=""/>
88 <param name="disable_identification_ms2_precursors" argument="-disable_identification_ms2_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if MS2-level precursor ions for identification should not be allowed for extraction of the precursor signal from the fragment ion data (MS2-level)" help=""/> 86 <param argument="-disable_identification_ms2_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if MS2-level precursor ions for identification should not be allowed for extraction of the precursor signal from the fragment ion data (MS2-level)" help=""/>
89 <param name="disable_identification_specific_losses" argument="-disable_identification_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if specific neutral losses for identification fragment ions should not be allowed" help=""/> 87 <param argument="-disable_identification_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if specific neutral losses for identification fragment ions should not be allowed" help=""/>
90 <param name="enable_identification_unspecific_losses" argument="-enable_identification_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help=""/> 88 <param argument="-enable_identification_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help=""/>
91 <param name="enable_swath_specifity" argument="-enable_swath_specifity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions without precursor specificity" help="(i.e. across whole precursor isolation window instead of precursor MZ) should be generated"/> 89 <param argument="-enable_swath_specifity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions without precursor specificity" help="(i.e. across whole precursor isolation window instead of precursor MZ) should be generated"/>
92 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 90 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
93 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 91 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
94 <expand macro="list_string_san"/> 92 <expand macro="list_string_san" name="test"/>
95 </param> 93 </param>
96 </expand> 94 </expand>
97 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 95 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
98 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 96 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
99 </param> 97 </param>
100 </inputs> 98 </inputs>
101 <outputs> 99 <outputs>
102 <data name="out" label="${tool.name} on ${on_string}: out"> 100 <data name="out" label="${tool.name} on ${on_string}: out" format="traml">
103 <change_format> 101 <change_format>
104 <when input="out_type" value="TraML" format="traml"/>
105 <when input="out_type" value="pqp" format="pqp"/> 102 <when input="out_type" value="pqp" format="pqp"/>
106 <when input="out_type" value="tsv" format="tabular"/> 103 <when input="out_type" value="tsv" format="tabular"/>
107 </change_format> 104 </change_format>
108 </data> 105 </data>
109 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 106 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
110 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 107 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
111 </data> 108 </data>
112 </outputs> 109 </outputs>
113 <tests> 110 <tests><!-- TOPP_OpenSwathAssayGenerator_test_1 -->
114 <expand macro="autotest_OpenSwathAssayGenerator"/> 111 <test expect_num_outputs="2">
115 <expand macro="manutest_OpenSwathAssayGenerator"/> 112 <section name="adv_opts">
113 <param name="max_num_alternative_localizations" value="10000"/>
114 <param name="disable_identification_ms2_precursors" value="false"/>
115 <param name="disable_identification_specific_losses" value="false"/>
116 <param name="enable_identification_unspecific_losses" value="false"/>
117 <param name="enable_swath_specifity" value="false"/>
118 <param name="force" value="false"/>
119 <param name="test" value="true"/>
120 </section>
121 <param name="in" value="OpenSwathAssayGenerator_input.TraML"/>
122 <output name="out" file="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
123 <param name="out_type" value="TraML"/>
124 <param name="min_transitions" value="6"/>
125 <param name="max_transitions" value="6"/>
126 <param name="allowed_fragment_types" value="b,y"/>
127 <param name="allowed_fragment_charges" value="2,3"/>
128 <param name="enable_detection_specific_losses" value="true"/>
129 <param name="enable_detection_unspecific_losses" value="false"/>
130 <param name="precursor_mz_threshold" value="0.025"/>
131 <param name="precursor_lower_mz_limit" value="400.0"/>
132 <param name="precursor_upper_mz_limit" value="1200.0"/>
133 <param name="product_mz_threshold" value="0.025"/>
134 <param name="product_lower_mz_limit" value="350.0"/>
135 <param name="product_upper_mz_limit" value="2000.0"/>
136 <param name="enable_ipf" value="false"/>
137 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
138 <output name="ctd_out" ftype="xml">
139 <assert_contents>
140 <is_valid_xml/>
141 </assert_contents>
142 </output>
143 </test>
144 <!-- TOPP_OpenSwathAssayGenerator_test_2 -->
145 <test expect_num_outputs="2">
146 <section name="adv_opts">
147 <param name="max_num_alternative_localizations" value="10000"/>
148 <param name="disable_identification_ms2_precursors" value="false"/>
149 <param name="disable_identification_specific_losses" value="false"/>
150 <param name="enable_identification_unspecific_losses" value="false"/>
151 <param name="enable_swath_specifity" value="false"/>
152 <param name="force" value="false"/>
153 <param name="test" value="true"/>
154 </section>
155 <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
156 <output name="out" file="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
157 <param name="out_type" value="TraML"/>
158 <param name="min_transitions" value="6"/>
159 <param name="max_transitions" value="6"/>
160 <param name="allowed_fragment_types" value="b,y"/>
161 <param name="allowed_fragment_charges" value="1,2,3,4"/>
162 <param name="enable_detection_specific_losses" value="false"/>
163 <param name="enable_detection_unspecific_losses" value="false"/>
164 <param name="precursor_mz_threshold" value="0.025"/>
165 <param name="precursor_lower_mz_limit" value="400.0"/>
166 <param name="precursor_upper_mz_limit" value="1200.0"/>
167 <param name="product_mz_threshold" value="0.025"/>
168 <param name="product_lower_mz_limit" value="350.0"/>
169 <param name="product_upper_mz_limit" value="2000.0"/>
170 <param name="unimod_file" value="OpenSwathAssayGenerator_input_2_unimod.xml"/>
171 <param name="enable_ipf" value="true"/>
172 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
173 <output name="ctd_out" ftype="xml">
174 <assert_contents>
175 <is_valid_xml/>
176 </assert_contents>
177 </output>
178 </test>
179 <!-- TOPP_OpenSwathAssayGenerator_test_3 -->
180 <test expect_num_outputs="2">
181 <section name="adv_opts">
182 <param name="max_num_alternative_localizations" value="10000"/>
183 <param name="disable_identification_ms2_precursors" value="false"/>
184 <param name="disable_identification_specific_losses" value="false"/>
185 <param name="enable_identification_unspecific_losses" value="false"/>
186 <param name="enable_swath_specifity" value="false"/>
187 <param name="force" value="false"/>
188 <param name="test" value="true"/>
189 </section>
190 <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
191 <output name="out" file="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
192 <param name="out_type" value="TraML"/>
193 <param name="min_transitions" value="6"/>
194 <param name="max_transitions" value="6"/>
195 <param name="allowed_fragment_types" value="b,y"/>
196 <param name="allowed_fragment_charges" value="1,2,3,4"/>
197 <param name="enable_detection_specific_losses" value="false"/>
198 <param name="enable_detection_unspecific_losses" value="false"/>
199 <param name="precursor_mz_threshold" value="0.025"/>
200 <param name="precursor_lower_mz_limit" value="400.0"/>
201 <param name="precursor_upper_mz_limit" value="1200.0"/>
202 <param name="product_mz_threshold" value="0.025"/>
203 <param name="product_lower_mz_limit" value="350.0"/>
204 <param name="product_upper_mz_limit" value="2000.0"/>
205 <param name="unimod_file" value="OpenSwathAssayGenerator_input_3_unimod.xml"/>
206 <param name="enable_ipf" value="true"/>
207 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
208 <output name="ctd_out" ftype="xml">
209 <assert_contents>
210 <is_valid_xml/>
211 </assert_contents>
212 </output>
213 </test>
116 </tests> 214 </tests>
117 <help><![CDATA[Generates assays according to different models for a specific TraML 215 <help><![CDATA[Generates assays according to different models for a specific TraML
118 216
119 217
120 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathAssayGenerator.html]]></help> 218 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathAssayGenerator.html]]></help>
121 <expand macro="references"/> 219 <expand macro="references"/>
122 </tool> 220 </tool>