comparison MascotAdapter.xml @ 13:27e308170367 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:12:19 +0000
parents 57fb2083a8cb
children 087b9d721a08
comparison
equal deleted inserted replaced
12:3dfa8cf579c5 13:27e308170367
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: [Identification]--> 3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="MascotAdapter" name="MascotAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="MascotAdapter" name="MascotAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Annotates MS/MS spectra using Mascot.</description> 5 <description>Annotates MS/MS spectra using Mascot.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MascotAdapter</token> 7 <token name="@EXECUTABLE@">MascotAdapter</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[{"mascot_directory": "TODO", "temp_data_directory": "\$TMP_DIR", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 39 <configfile name="hardcoded_json"><![CDATA[{"mascot_directory": "TODO", "temp_data_directory": "\$TMP_DIR", "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="mascotxml,mzdata" optional="false" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/> 42 <param argument="-in" type="data" format="mascotxml,mzdata" optional="false" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/>
45 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="output file type (for TOPPAS)" help=""> 43 <param argument="-out_type" display="radio" type="select" optional="false" label="output file type (for TOPPAS)" help="">
46 <option value="idXML">idxml</option> 44 <option value="idXML">idxml</option>
47 <option value="mgf">mgf</option> 45 <option value="mgf">mgf</option>
48 <expand macro="list_string_san"/> 46 <expand macro="list_string_san" name="out_type"/>
49 </param> 47 </param>
50 <param name="instrument" argument="-instrument" type="text" optional="true" value="Default" label="the instrument that was used to measure the spectra" help=""> 48 <param argument="-instrument" type="text" optional="true" value="Default" label="the instrument that was used to measure the spectra" help="">
51 <expand macro="list_string_san"/> 49 <expand macro="list_string_san" name="instrument"/>
52 </param> 50 </param>
53 <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="2.0" label="the precursor mass tolerance" help=""/> 51 <param argument="-precursor_mass_tolerance" type="float" optional="true" value="2.0" label="the precursor mass tolerance" help=""/>
54 <param name="peak_mass_tolerance" argument="-peak_mass_tolerance" type="float" optional="true" value="1.0" label="the peak mass tolerance" help=""/> 52 <param argument="-peak_mass_tolerance" type="float" optional="true" value="1.0" label="the peak mass tolerance" help=""/>
55 <param name="taxonomy" argument="-taxonomy" type="select" optional="false" label="the taxonomy" help=""> 53 <param argument="-taxonomy" type="select" optional="true" label="the taxonomy" help="">
56 <option value="All entries" selected="true">All entries</option> 54 <option value="All entries" selected="true">All entries</option>
57 <option value=". . Archaea (Archaeobacteria)">. . Archaea (Archaeobacteria)</option> 55 <option value=". . Archaea (Archaeobacteria)">. . Archaea (Archaeobacteria)</option>
58 <option value=". . Eukaryota (eucaryotes)">. . Eukaryota (eucaryotes)</option> 56 <option value=". . Eukaryota (eucaryotes)">. . Eukaryota (eucaryotes)</option>
59 <option value=". . . . Alveolata (alveolates)">. . . . Alveolata (alveolates)</option> 57 <option value=". . . . Alveolata (alveolates)">. . . . Alveolata (alveolates)</option>
60 <option value=". . . . . . Plasmodium falciparum (malaria parasite)">. . . . . . Plasmodium falciparum (malaria parasite)</option> 58 <option value=". . . . . . Plasmodium falciparum (malaria parasite)">. . . . . . Plasmodium falciparum (malaria parasite)</option>
116 <option value=". . . . Hepatitis C virus">. . . . Hepatitis C virus</option> 114 <option value=". . . . Hepatitis C virus">. . . . Hepatitis C virus</option>
117 <option value=". . . . Other viruses">. . . . Other viruses</option> 115 <option value=". . . . Other viruses">. . . . Other viruses</option>
118 <option value=". . Other (includes plasmids and artificial sequences)">. . Other (includes plasmids and artificial sequences)</option> 116 <option value=". . Other (includes plasmids and artificial sequences)">. . Other (includes plasmids and artificial sequences)</option>
119 <option value=". . unclassified">. . unclassified</option> 117 <option value=". . unclassified">. . unclassified</option>
120 <option value=". . Species information unavailable">. . Species information unavailable</option> 118 <option value=". . Species information unavailable">. . Species information unavailable</option>
121 <expand macro="list_string_san"/> 119 <expand macro="list_string_san" name="taxonomy"/>
122 </param> 120 </param>
123 <param name="modifications" argument="-modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 121 <param argument="-modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
124 <expand macro="list_string_val"/> 122 <expand macro="list_string_val" name="modifications"/>
125 <expand macro="list_string_san"/> 123 <expand macro="list_string_san" name="modifications"/>
126 </param> 124 </param>
127 <param name="variable_modifications" argument="-variable_modifications" type="text" optional="true" value="" label="the variable modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 125 <param argument="-variable_modifications" type="text" optional="true" value="" label="the variable modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
128 <expand macro="list_string_val"/> 126 <expand macro="list_string_val" name="variable_modifications"/>
129 <expand macro="list_string_san"/> 127 <expand macro="list_string_san" name="variable_modifications"/>
130 </param> 128 </param>
131 <param name="charges" argument="-charges" type="text" optional="true" value="1+ 2+ 3+" label="the different charge states" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 129 <param argument="-charges" type="text" optional="true" value="1+ 2+ 3+" label="the different charge states" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
132 <expand macro="list_string_val"/> 130 <expand macro="list_string_val" name="charges"/>
133 <expand macro="list_string_san"/> 131 <expand macro="list_string_san" name="charges"/>
134 </param> 132 </param>
135 <param name="db" argument="-db" type="text" optional="true" value="MSDB" label="the database to search in" help=""> 133 <param argument="-db" type="text" optional="true" value="MSDB" label="the database to search in" help="">
136 <expand macro="list_string_san"/> 134 <expand macro="list_string_san" name="db"/>
137 </param> 135 </param>
138 <param name="hits" argument="-hits" type="text" optional="true" value="AUTO" label="the number of hits to report" help=""> 136 <param argument="-hits" type="text" optional="true" value="AUTO" label="the number of hits to report" help="">
139 <expand macro="list_string_san"/> 137 <expand macro="list_string_san" name="hits"/>
140 </param> 138 </param>
141 <param name="cleavage" argument="-cleavage" type="select" optional="false" label="The enzyme descriptor to the enzyme used for digestion" help="(Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)"> 139 <param argument="-cleavage" type="select" optional="true" label="The enzyme descriptor to the enzyme used for digestion" help="(Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)">
142 <option value="Trypsin" selected="true">Trypsin</option> 140 <option value="Trypsin" selected="true">Trypsin</option>
143 <option value="Arg-C">Arg-C</option> 141 <option value="Arg-C">Arg-C</option>
144 <option value="Asp-N">Asp-N</option> 142 <option value="Asp-N">Asp-N</option>
145 <option value="Asp-N_ambic">Asp-N_ambic</option> 143 <option value="Asp-N_ambic">Asp-N_ambic</option>
146 <option value="Chymotrypsin">Chymotrypsin</option> 144 <option value="Chymotrypsin">Chymotrypsin</option>
156 <option value="V8-DE">V8-DE</option> 154 <option value="V8-DE">V8-DE</option>
157 <option value="V8-E">V8-E</option> 155 <option value="V8-E">V8-E</option>
158 <option value="semiTrypsin">semiTrypsin</option> 156 <option value="semiTrypsin">semiTrypsin</option>
159 <option value="LysC+AspN">LysC+AspN</option> 157 <option value="LysC+AspN">LysC+AspN</option>
160 <option value="None">None</option> 158 <option value="None">None</option>
161 <expand macro="list_string_san"/> 159 <expand macro="list_string_san" name="cleavage"/>
162 </param> 160 </param>
163 <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" value="0" label="number of allowed missed cleavages" help=""/> 161 <param argument="-missed_cleavages" type="integer" optional="true" min="0" value="0" label="number of allowed missed cleavages" help=""/>
164 <param name="sig_threshold" argument="-sig_threshold" type="float" optional="true" value="0.05" label="significance threshold" help=""/> 162 <param argument="-sig_threshold" type="float" optional="true" value="0.05" label="significance threshold" help=""/>
165 <param name="pep_homol" argument="-pep_homol" type="float" optional="true" value="1.0" label="peptide homology threshold" help=""/> 163 <param argument="-pep_homol" type="float" optional="true" value="1.0" label="peptide homology threshold" help=""/>
166 <param name="pep_ident" argument="-pep_ident" type="float" optional="true" value="1.0" label="peptide ident threshold" help=""/> 164 <param argument="-pep_ident" type="float" optional="true" value="1.0" label="peptide ident threshold" help=""/>
167 <param name="pep_rank" argument="-pep_rank" type="integer" optional="true" value="1" label="peptide rank" help=""/> 165 <param argument="-pep_rank" type="integer" optional="true" value="1" label="peptide rank" help=""/>
168 <param name="prot_score" argument="-prot_score" type="float" optional="true" value="1.0" label="protein score" help=""/> 166 <param argument="-prot_score" type="float" optional="true" value="1.0" label="protein score" help=""/>
169 <param name="pep_score" argument="-pep_score" type="float" optional="true" value="1.0" label="peptide score" help=""/> 167 <param argument="-pep_score" type="float" optional="true" value="1.0" label="peptide score" help=""/>
170 <param name="pep_exp_z" argument="-pep_exp_z" type="integer" optional="true" value="1" label="peptide expected charge" help=""/> 168 <param argument="-pep_exp_z" type="integer" optional="true" value="1" label="peptide expected charge" help=""/>
171 <param name="show_unassigned" argument="-show_unassigned" type="integer" optional="true" value="1" label="show_unassigned" help=""/> 169 <param argument="-show_unassigned" type="integer" optional="true" value="1" label="show_unassigned" help=""/>
172 <param name="first_dim_rt" argument="-first_dim_rt" type="float" optional="true" value="0.0" label="additional information which is added to every peptide identification as metavalue if set &gt; 0" help=""/> 170 <param argument="-first_dim_rt" type="float" optional="true" value="0.0" label="additional information which is added to every peptide identification as metavalue if set &gt; 0" help=""/>
173 <param name="boundary" argument="-boundary" type="text" optional="true" value="" label="MIME boundary for mascot output format" help=""> 171 <param argument="-boundary" type="text" optional="true" value="" label="MIME boundary for mascot output format" help="">
174 <expand macro="list_string_san"/> 172 <expand macro="list_string_san" name="boundary"/>
175 </param> 173 </param>
176 <param name="mass_type" argument="-mass_type" display="radio" type="select" optional="false" label="mass type" help=""> 174 <param argument="-mass_type" type="select" optional="true" label="mass type" help="">
177 <option value="Monoisotopic" selected="true">Monoisotopic</option> 175 <option value="Monoisotopic" selected="true">Monoisotopic</option>
178 <option value="Average">Average</option> 176 <option value="Average">Average</option>
179 <expand macro="list_string_san"/> 177 <expand macro="list_string_san" name="mass_type"/>
180 </param> 178 </param>
181 <expand macro="adv_opts_macro"> 179 <expand macro="adv_opts_macro">
182 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 180 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
183 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 181 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
184 <expand macro="list_string_san"/> 182 <expand macro="list_string_san" name="test"/>
185 </param> 183 </param>
186 </expand> 184 </expand>
187 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 185 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
188 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 186 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
189 </param> 187 </param>
190 </inputs> 188 </inputs>
191 <outputs> 189 <outputs>
192 <data name="out" label="${tool.name} on ${on_string}: out"> 190 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml">
193 <change_format> 191 <change_format>
194 <when input="out_type" value="idXML" format="idxml"/>
195 <when input="out_type" value="mgf" format="mgf"/> 192 <when input="out_type" value="mgf" format="mgf"/>
196 </change_format> 193 </change_format>
197 </data> 194 </data>
198 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 195 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
199 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 196 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
200 </data> 197 </data>
201 </outputs> 198 </outputs>
202 <tests> 199 <tests><!-- TOPP_MascotAdapter_1 -->
203 <expand macro="autotest_MascotAdapter"/> 200 <test expect_num_outputs="2">
204 <expand macro="manutest_MascotAdapter"/> 201 <section name="adv_opts">
202 <param name="force" value="false"/>
203 <param name="test" value="true"/>
204 </section>
205 <param name="in" value="MascotAdapter_1_input.mzData"/>
206 <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta_frac="0.7"/>
207 <param name="out_type" value="mgf"/>
208 <param name="instrument" value="ESI-TRAP"/>
209 <param name="precursor_mass_tolerance" value="1.3"/>
210 <param name="peak_mass_tolerance" value="0.3"/>
211 <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/>
212 <param name="modifications" value="&quot;Carboxymethyl (C)&quot;"/>
213 <param name="variable_modifications" value="&quot;Variable_Modifications_TEST_1&quot;"/>
214 <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
215 <param name="db" value="MSDB"/>
216 <param name="hits" value="AUTO"/>
217 <param name="cleavage" value="Trypsin"/>
218 <param name="missed_cleavages" value="1"/>
219 <param name="sig_threshold" value="0.05"/>
220 <param name="pep_homol" value="1.0"/>
221 <param name="pep_ident" value="1.0"/>
222 <param name="pep_rank" value="1"/>
223 <param name="prot_score" value="1.0"/>
224 <param name="pep_score" value="1.0"/>
225 <param name="pep_exp_z" value="1"/>
226 <param name="show_unassigned" value="1"/>
227 <param name="first_dim_rt" value="0.0"/>
228 <param name="boundary" value="ABCDEFGHIJKMNOPQRSTUVWXYZ"/>
229 <param name="mass_type" value="Monoisotopic"/>
230 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
231 <output name="ctd_out" ftype="xml">
232 <assert_contents>
233 <is_valid_xml/>
234 </assert_contents>
235 </output>
236 </test>
237 <!-- TOPP_MascotAdapter_2 -->
238 <test expect_num_outputs="2">
239 <section name="adv_opts">
240 <param name="force" value="false"/>
241 <param name="test" value="true"/>
242 </section>
243 <param name="in" value="MascotAdapter_2_input.mascotXML"/>
244 <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
245 <param name="out_type" value="idXML"/>
246 <param name="instrument" value="Default"/>
247 <param name="precursor_mass_tolerance" value="2.0"/>
248 <param name="peak_mass_tolerance" value="1.0"/>
249 <param name="taxonomy" value="All entries"/>
250 <param name="modifications" value=""/>
251 <param name="variable_modifications" value=""/>
252 <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
253 <param name="db" value="MSDB"/>
254 <param name="hits" value="AUTO"/>
255 <param name="cleavage" value="Trypsin"/>
256 <param name="missed_cleavages" value="0"/>
257 <param name="sig_threshold" value="0.05"/>
258 <param name="pep_homol" value="1.0"/>
259 <param name="pep_ident" value="1.0"/>
260 <param name="pep_rank" value="1"/>
261 <param name="prot_score" value="1.0"/>
262 <param name="pep_score" value="1.0"/>
263 <param name="pep_exp_z" value="1"/>
264 <param name="show_unassigned" value="1"/>
265 <param name="first_dim_rt" value="0.0"/>
266 <param name="boundary" value=""/>
267 <param name="mass_type" value="Monoisotopic"/>
268 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
269 <output name="ctd_out" ftype="xml">
270 <assert_contents>
271 <is_valid_xml/>
272 </assert_contents>
273 </output>
274 </test>
205 </tests> 275 </tests>
206 <help><![CDATA[Annotates MS/MS spectra using Mascot. 276 <help><![CDATA[Annotates MS/MS spectra using Mascot.
207 277
208 278
209 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MascotAdapter.html]]></help> 279 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MascotAdapter.html]]></help>
210 <expand macro="references"/> 280 <expand macro="references"/>
211 </tool> 281 </tool>