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comparison IDMapper.xml @ 15:adca857b4884 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 19:05:34 +0000
parents 2517c03f5cd3
children ea02403ff738
comparison
equal deleted inserted replaced
14:39caaa778d2e 15:adca857b4884
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: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="IDMapper" name="IDMapper" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="IDMapper" name="IDMapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Assigns protein/peptide identifications to features or consensus features.</description> 5 <description>Assigns protein/peptide identifications to features or consensus features.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">IDMapper</token> 7 <token name="@EXECUTABLE@">IDMapper</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@
51 <configfiles> 49 <configfiles>
52 <inputs name="args_json" data_style="paths"/> 50 <inputs name="args_json" data_style="paths"/>
53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 51 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
54 </configfiles> 52 </configfiles>
55 <inputs> 53 <inputs>
56 <param name="id" argument="-id" type="data" format="idxml,mzid" optional="false" label="Protein/peptide identifications file" help=" select idxml,mzid data sets(s)"/> 54 <param argument="-id" type="data" format="idxml,mzid" optional="false" label="Protein/peptide identifications file" help=" select idxml,mzid data sets(s)"/>
57 <param name="in" argument="-in" type="data" format="consensusxml,featurexml,mzq" optional="false" label="Feature map/consensus map file" help=" select consensusxml,featurexml,mzq data sets(s)"/> 55 <param argument="-in" type="data" format="consensusxml,featurexml,mzq" optional="false" label="Feature map/consensus map file" help=" select consensusxml,featurexml,mzq data sets(s)"/>
58 <param name="rt_tolerance" argument="-rt_tolerance" type="float" optional="true" min="0.0" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/> 56 <param argument="-rt_tolerance" type="float" optional="true" min="0.0" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
59 <param name="mz_tolerance" argument="-mz_tolerance" type="float" optional="true" min="0.0" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/> 57 <param argument="-mz_tolerance" type="float" optional="true" min="0.0" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
60 <param name="mz_measure" argument="-mz_measure" display="radio" type="select" optional="false" label="Unit of 'mz_tolerance'" help=""> 58 <param argument="-mz_measure" type="select" optional="true" label="Unit of 'mz_tolerance'" help="">
61 <option value="ppm" selected="true">ppm</option> 59 <option value="ppm" selected="true">ppm</option>
62 <option value="Da">Da</option> 60 <option value="Da">Da</option>
63 <expand macro="list_string_san"/> 61 <expand macro="list_string_san" name="mz_measure"/>
64 </param> 62 </param>
65 <param name="mz_reference" argument="-mz_reference" display="radio" type="select" optional="false" label="Source of m/z values for peptide identifications" help="If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',. masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.. ('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)"> 63 <param argument="-mz_reference" type="select" optional="true" label="Source of m/z values for peptide identifications" help="If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',. masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.. ('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)">
66 <option value="precursor">precursor</option> 64 <option value="precursor">precursor</option>
67 <option value="peptide" selected="true">peptide</option> 65 <option value="peptide" selected="true">peptide</option>
68 <expand macro="list_string_san"/> 66 <expand macro="list_string_san" name="mz_reference"/>
69 </param> 67 </param>
70 <section name="feature" title="Additional options for featureXML input" help="" expanded="false"> 68 <section name="feature" title="Additional options for featureXML input" help="" expanded="false">
71 <param name="use_centroid_rt" argument="-feature:use_centroid_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces" help=""/> 69 <param name="use_centroid_rt" argument="-feature:use_centroid_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces" help=""/>
72 <param name="use_centroid_mz" argument="-feature:use_centroid_mz" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces" help="(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)"/> 70 <param name="use_centroid_mz" argument="-feature:use_centroid_mz" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces" help="(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)"/>
73 </section> 71 </section>
77 </section> 75 </section>
78 <section name="spectra" title="Additional options for mzML input" help="" expanded="false"> 76 <section name="spectra" title="Additional options for mzML input" help="" expanded="false">
79 <param name="_in" argument="-spectra:_in" type="data" format="mzml" optional="true" label="MS run used to annotated unidentified spectra to features or consensus features" help=" select mzml data sets(s)"/> 77 <param name="_in" argument="-spectra:_in" type="data" format="mzml" optional="true" label="MS run used to annotated unidentified spectra to features or consensus features" help=" select mzml data sets(s)"/>
80 </section> 78 </section>
81 <expand macro="adv_opts_macro"> 79 <expand macro="adv_opts_macro">
82 <param name="ignore_charge" argument="-ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature" help=""/> 80 <param argument="-ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature" help=""/>
83 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 81 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
84 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 82 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
85 <expand macro="list_string_san"/> 83 <expand macro="list_string_san" name="test"/>
86 </param> 84 </param>
87 </expand> 85 </expand>
88 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 86 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
89 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 87 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
90 </param> 88 </param>
93 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/> 91 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/>
94 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 92 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
95 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 93 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
96 </data> 94 </data>
97 </outputs> 95 </outputs>
98 <tests> 96 <tests><!-- TOPP_IDMapper_1 -->
99 <expand macro="autotest_IDMapper"/> 97 <test expect_num_outputs="2">
100 <expand macro="manutest_IDMapper"/> 98 <section name="adv_opts">
99 <param name="ignore_charge" value="true"/>
100 <param name="force" value="false"/>
101 <param name="test" value="true"/>
102 </section>
103 <param name="id" value="IDMapper_1_input.idXML"/>
104 <param name="in" value="IDMapper_1_input.featureXML"/>
105 <output name="out" file="IDMapper_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
106 <param name="rt_tolerance" value="5.0"/>
107 <param name="mz_tolerance" value="1.0"/>
108 <param name="mz_measure" value="Da"/>
109 <param name="mz_reference" value="precursor"/>
110 <section name="feature">
111 <param name="use_centroid_rt" value="false"/>
112 <param name="use_centroid_mz" value="false"/>
113 </section>
114 <section name="consensus">
115 <param name="use_subelements" value="false"/>
116 <param name="annotate_ids_with_subelements" value="false"/>
117 </section>
118 <section name="spectra"/>
119 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
120 <output name="ctd_out" ftype="xml">
121 <assert_contents>
122 <is_valid_xml/>
123 </assert_contents>
124 </output>
125 </test>
126 <!-- TOPP_IDMapper_2 -->
127 <test expect_num_outputs="2">
128 <section name="adv_opts">
129 <param name="ignore_charge" value="false"/>
130 <param name="force" value="false"/>
131 <param name="test" value="true"/>
132 </section>
133 <param name="id" value="IDMapper_2_input.idXML"/>
134 <param name="in" value="IDMapper_2_input.consensusXML"/>
135 <output name="out" file="IDMapper_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
136 <param name="rt_tolerance" value="5.0"/>
137 <param name="mz_tolerance" value="1.0"/>
138 <param name="mz_measure" value="Da"/>
139 <param name="mz_reference" value="precursor"/>
140 <section name="feature">
141 <param name="use_centroid_rt" value="false"/>
142 <param name="use_centroid_mz" value="true"/>
143 </section>
144 <section name="consensus">
145 <param name="use_subelements" value="false"/>
146 <param name="annotate_ids_with_subelements" value="false"/>
147 </section>
148 <section name="spectra"/>
149 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
150 <output name="ctd_out" ftype="xml">
151 <assert_contents>
152 <is_valid_xml/>
153 </assert_contents>
154 </output>
155 </test>
156 <!-- TOPP_IDMapper_3 -->
157 <test expect_num_outputs="2">
158 <section name="adv_opts">
159 <param name="ignore_charge" value="true"/>
160 <param name="force" value="false"/>
161 <param name="test" value="true"/>
162 </section>
163 <param name="id" value="IDMapper_3_input.idXML"/>
164 <param name="in" value="IDMapper_3_input.featureXML"/>
165 <output name="out" file="IDMapper_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
166 <param name="rt_tolerance" value="4.0"/>
167 <param name="mz_tolerance" value="3.0"/>
168 <param name="mz_measure" value="ppm"/>
169 <param name="mz_reference" value="precursor"/>
170 <section name="feature">
171 <param name="use_centroid_rt" value="false"/>
172 <param name="use_centroid_mz" value="true"/>
173 </section>
174 <section name="consensus">
175 <param name="use_subelements" value="false"/>
176 <param name="annotate_ids_with_subelements" value="false"/>
177 </section>
178 <section name="spectra"/>
179 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
180 <output name="ctd_out" ftype="xml">
181 <assert_contents>
182 <is_valid_xml/>
183 </assert_contents>
184 </output>
185 </test>
186 <!-- TOPP_IDMapper_4 -->
187 <test expect_num_outputs="2">
188 <section name="adv_opts">
189 <param name="ignore_charge" value="false"/>
190 <param name="force" value="false"/>
191 <param name="test" value="true"/>
192 </section>
193 <param name="id" value="IDMapper_4_input.idXML"/>
194 <param name="in" value="IDMapper_4_input.featureXML"/>
195 <output name="out" file="IDMapper_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
196 <param name="rt_tolerance" value="10.0"/>
197 <param name="mz_tolerance" value="20.0"/>
198 <param name="mz_measure" value="ppm"/>
199 <param name="mz_reference" value="peptide"/>
200 <section name="feature">
201 <param name="use_centroid_rt" value="false"/>
202 <param name="use_centroid_mz" value="true"/>
203 </section>
204 <section name="consensus">
205 <param name="use_subelements" value="false"/>
206 <param name="annotate_ids_with_subelements" value="false"/>
207 </section>
208 <section name="spectra">
209 <param name="_in" value="IDMapper_4_input.mzML"/>
210 </section>
211 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
212 <output name="ctd_out" ftype="xml">
213 <assert_contents>
214 <is_valid_xml/>
215 </assert_contents>
216 </output>
217 </test>
218 <!-- TOPP_IDMapper_5 -->
219 <test expect_num_outputs="2">
220 <section name="adv_opts">
221 <param name="ignore_charge" value="false"/>
222 <param name="force" value="false"/>
223 <param name="test" value="true"/>
224 </section>
225 <param name="id" value="IDMapper_5_input.idXML"/>
226 <param name="in" value="IDMapper_5_input.featureXML"/>
227 <output name="out" file="IDMapper_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
228 <param name="rt_tolerance" value="20.0"/>
229 <param name="mz_tolerance" value="10.0"/>
230 <param name="mz_measure" value="ppm"/>
231 <param name="mz_reference" value="peptide"/>
232 <section name="feature">
233 <param name="use_centroid_rt" value="false"/>
234 <param name="use_centroid_mz" value="false"/>
235 </section>
236 <section name="consensus">
237 <param name="use_subelements" value="false"/>
238 <param name="annotate_ids_with_subelements" value="false"/>
239 </section>
240 <section name="spectra">
241 <param name="_in" value="IDMapper_5_input.mzML"/>
242 </section>
243 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
244 <output name="ctd_out" ftype="xml">
245 <assert_contents>
246 <is_valid_xml/>
247 </assert_contents>
248 </output>
249 </test>
101 </tests> 250 </tests>
102 <help><![CDATA[Assigns protein/peptide identifications to features or consensus features. 251 <help><![CDATA[Assigns protein/peptide identifications to features or consensus features.
103 252
104 253
105 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_IDMapper.html]]></help> 254 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDMapper.html]]></help>
106 <expand macro="references"/> 255 <expand macro="references"/>
107 </tool> 256 </tool>