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comparison MascotAdapter.xml @ 14:087b9d721a08 draft default tip

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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 21:43:35 +0000
parents 27e308170367
children
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13:27e308170367 14:087b9d721a08
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: [Identification]--> 2 <!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
4 <tool id="MascotAdapter" name="MascotAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="MascotAdapter" name="MascotAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Annotates MS/MS spectra using Mascot.</description> 4 <description>Annotates MS/MS spectra using Mascot</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">MascotAdapter</token> 6 <token name="@EXECUTABLE@">MascotAdapter</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
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[{"mascot_directory": "TODO", "temp_data_directory": "\$TMP_DIR", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 38 <configfile name="hardcoded_json"><![CDATA[{"mascot_directory": "TODO", "temp_data_directory": "\$TMP_DIR", "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="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)"/> 41 <param argument="-in" type="data" format="mascotxml,mzdata" 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)"/>
43 <param argument="-out_type" display="radio" type="select" optional="false" label="output file type (for TOPPAS)" help=""> 42 <param argument="-out_type" type="select" label="output file type (for TOPPAS)" help="">
44 <option value="idXML">idxml</option> 43 <option value="idXML">idxml</option>
45 <option value="mgf">mgf</option> 44 <option value="mgf">mgf</option>
45 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
46 <expand macro="list_string_san" name="out_type"/> 46 <expand macro="list_string_san" name="out_type"/>
47 </param> 47 </param>
48 <param 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" value="Default" label="the instrument that was used to measure the spectra" help="">
49 <expand macro="list_string_san" name="instrument"/> 49 <expand macro="list_string_san" name="instrument"/>
50 </param> 50 </param>
51 <param 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" value="2.0" label="the precursor mass tolerance" help=""/>
52 <param 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" value="1.0" label="the peak mass tolerance" help=""/>
53 <param argument="-taxonomy" type="select" optional="true" label="the taxonomy" help=""> 53 <param argument="-taxonomy" type="select" label="the taxonomy" help="">
54 <option value="All entries" selected="true">All entries</option> 54 <option value="All entries" selected="true">All entries</option>
55 <option value=". . Archaea (Archaeobacteria)">. . Archaea (Archaeobacteria)</option> 55 <option value=". . Archaea (Archaeobacteria)">. . Archaea (Archaeobacteria)</option>
56 <option value=". . Eukaryota (eucaryotes)">. . Eukaryota (eucaryotes)</option> 56 <option value=". . Eukaryota (eucaryotes)">. . Eukaryota (eucaryotes)</option>
57 <option value=". . . . Alveolata (alveolates)">. . . . Alveolata (alveolates)</option> 57 <option value=". . . . Alveolata (alveolates)">. . . . Alveolata (alveolates)</option>
58 <option value=". . . . . . Plasmodium falciparum (malaria parasite)">. . . . . . Plasmodium falciparum (malaria parasite)</option> 58 <option value=". . . . . . Plasmodium falciparum (malaria parasite)">. . . . . . Plasmodium falciparum (malaria parasite)</option>
124 </param> 124 </param>
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)"> 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)">
126 <expand macro="list_string_val" name="variable_modifications"/> 126 <expand macro="list_string_val" name="variable_modifications"/>
127 <expand macro="list_string_san" name="variable_modifications"/> 127 <expand macro="list_string_san" name="variable_modifications"/>
128 </param> 128 </param>
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)"> 129 <param argument="-charges" type="text" 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)">
130 <expand macro="list_string_val" name="charges"/> 130 <expand macro="list_string_val" name="charges"/>
131 <expand macro="list_string_san" name="charges"/> 131 <expand macro="list_string_san" name="charges"/>
132 </param> 132 </param>
133 <param argument="-db" type="text" optional="true" value="MSDB" label="the database to search in" help=""> 133 <param argument="-db" type="text" value="MSDB" label="the database to search in" help="">
134 <expand macro="list_string_san" name="db"/> 134 <expand macro="list_string_san" name="db"/>
135 </param> 135 </param>
136 <param argument="-hits" type="text" optional="true" value="AUTO" label="the number of hits to report" help=""> 136 <param argument="-hits" type="text" value="AUTO" label="the number of hits to report" help="">
137 <expand macro="list_string_san" name="hits"/> 137 <expand macro="list_string_san" name="hits"/>
138 </param> 138 </param>
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)"> 139 <param argument="-cleavage" type="select" 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)">
140 <option value="Trypsin" selected="true">Trypsin</option> 140 <option value="Trypsin" selected="true">Trypsin</option>
141 <option value="Arg-C">Arg-C</option> 141 <option value="Arg-C">Arg-C</option>
142 <option value="Asp-N">Asp-N</option> 142 <option value="Asp-N">Asp-N</option>
143 <option value="Asp-N_ambic">Asp-N_ambic</option> 143 <option value="Asp-N_ambic">Asp-N_ambic</option>
144 <option value="Chymotrypsin">Chymotrypsin</option> 144 <option value="Chymotrypsin">Chymotrypsin</option>
156 <option value="semiTrypsin">semiTrypsin</option> 156 <option value="semiTrypsin">semiTrypsin</option>
157 <option value="LysC+AspN">LysC+AspN</option> 157 <option value="LysC+AspN">LysC+AspN</option>
158 <option value="None">None</option> 158 <option value="None">None</option>
159 <expand macro="list_string_san" name="cleavage"/> 159 <expand macro="list_string_san" name="cleavage"/>
160 </param> 160 </param>
161 <param 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" min="0" value="0" label="number of allowed missed cleavages" help=""/>
162 <param argument="-sig_threshold" type="float" optional="true" value="0.05" label="significance threshold" help=""/> 162 <param argument="-sig_threshold" type="float" value="0.05" label="significance threshold" help=""/>
163 <param argument="-pep_homol" type="float" optional="true" value="1.0" label="peptide homology threshold" help=""/> 163 <param argument="-pep_homol" type="float" value="1.0" label="peptide homology threshold" help=""/>
164 <param argument="-pep_ident" type="float" optional="true" value="1.0" label="peptide ident threshold" help=""/> 164 <param argument="-pep_ident" type="float" value="1.0" label="peptide ident threshold" help=""/>
165 <param argument="-pep_rank" type="integer" optional="true" value="1" label="peptide rank" help=""/> 165 <param argument="-pep_rank" type="integer" value="1" label="peptide rank" help=""/>
166 <param argument="-prot_score" type="float" optional="true" value="1.0" label="protein score" help=""/> 166 <param argument="-prot_score" type="float" value="1.0" label="protein score" help=""/>
167 <param argument="-pep_score" type="float" optional="true" value="1.0" label="peptide score" help=""/> 167 <param argument="-pep_score" type="float" value="1.0" label="peptide score" help=""/>
168 <param argument="-pep_exp_z" type="integer" optional="true" value="1" label="peptide expected charge" help=""/> 168 <param argument="-pep_exp_z" type="integer" value="1" label="peptide expected charge" help=""/>
169 <param argument="-show_unassigned" type="integer" optional="true" value="1" label="show_unassigned" help=""/> 169 <param argument="-show_unassigned" type="integer" value="1" label="show_unassigned" 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=""/> 170 <param argument="-first_dim_rt" type="float" value="0.0" label="additional information which is added to every peptide identification as metavalue if set &gt; 0" help=""/>
171 <param 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="">
172 <expand macro="list_string_san" name="boundary"/> 172 <expand macro="list_string_san" name="boundary"/>
173 </param> 173 </param>
174 <param argument="-mass_type" type="select" optional="true" label="mass type" help=""> 174 <param argument="-mass_type" type="select" label="mass type" help="">
175 <option value="Monoisotopic" selected="true">Monoisotopic</option> 175 <option value="Monoisotopic" selected="true">Monoisotopic</option>
176 <option value="Average">Average</option> 176 <option value="Average">Average</option>
177 <expand macro="list_string_san" name="mass_type"/> 177 <expand macro="list_string_san" name="mass_type"/>
178 </param> 178 </param>
179 <expand macro="adv_opts_macro"> 179 <expand macro="adv_opts_macro">
180 <param 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=""/>
181 <param 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" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
182 <expand macro="list_string_san" name="test"/> 182 <expand macro="list_string_san" name="test"/>
183 </param> 183 </param>
184 </expand> 184 </expand>
185 <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">
186 <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>
194 </data> 194 </data>
195 <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">
196 <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>
197 </data> 197 </data>
198 </outputs> 198 </outputs>
199 <tests><!-- TOPP_MascotAdapter_1 --> 199 <tests>
200 <!-- TOPP_MascotAdapter_1 -->
200 <test expect_num_outputs="2"> 201 <test expect_num_outputs="2">
201 <section name="adv_opts"> 202 <section name="adv_opts">
202 <param name="force" value="false"/> 203 <param name="force" value="false"/>
203 <param name="test" value="true"/> 204 <param name="test" value="true"/>
204 </section> 205 </section>
205 <param name="in" value="MascotAdapter_1_input.mzData"/> 206 <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 <output name="out" value="MascotAdapter_1_output.mascot_in" compare="sim_size" delta_frac="0.7"/>
207 <param name="out_type" value="mgf"/> 208 <param name="out_type" value="mgf"/>
208 <param name="instrument" value="ESI-TRAP"/> 209 <param name="instrument" value="ESI-TRAP"/>
209 <param name="precursor_mass_tolerance" value="1.3"/> 210 <param name="precursor_mass_tolerance" value="1.3"/>
210 <param name="peak_mass_tolerance" value="0.3"/> 211 <param name="peak_mass_tolerance" value="0.3"/>
211 <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/> 212 <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/>
231 <output name="ctd_out" ftype="xml"> 232 <output name="ctd_out" ftype="xml">
232 <assert_contents> 233 <assert_contents>
233 <is_valid_xml/> 234 <is_valid_xml/>
234 </assert_contents> 235 </assert_contents>
235 </output> 236 </output>
237 <assert_stdout>
238 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
239 </assert_stdout>
236 </test> 240 </test>
237 <!-- TOPP_MascotAdapter_2 --> 241 <!-- TOPP_MascotAdapter_2 -->
238 <test expect_num_outputs="2"> 242 <test expect_num_outputs="2">
239 <section name="adv_opts"> 243 <section name="adv_opts">
240 <param name="force" value="false"/> 244 <param name="force" value="false"/>
241 <param name="test" value="true"/> 245 <param name="test" value="true"/>
242 </section> 246 </section>
243 <param name="in" value="MascotAdapter_2_input.mascotXML"/> 247 <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"/> 248 <output name="out" value="MascotAdapter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
245 <param name="out_type" value="idXML"/> 249 <param name="out_type" value="idXML"/>
246 <param name="instrument" value="Default"/> 250 <param name="instrument" value="Default"/>
247 <param name="precursor_mass_tolerance" value="2.0"/> 251 <param name="precursor_mass_tolerance" value="2.0"/>
248 <param name="peak_mass_tolerance" value="1.0"/> 252 <param name="peak_mass_tolerance" value="1.0"/>
249 <param name="taxonomy" value="All entries"/> 253 <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;"/> 254 <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
253 <param name="db" value="MSDB"/> 255 <param name="db" value="MSDB"/>
254 <param name="hits" value="AUTO"/> 256 <param name="hits" value="AUTO"/>
255 <param name="cleavage" value="Trypsin"/> 257 <param name="cleavage" value="Trypsin"/>
256 <param name="missed_cleavages" value="0"/> 258 <param name="missed_cleavages" value="0"/>
269 <output name="ctd_out" ftype="xml"> 271 <output name="ctd_out" ftype="xml">
270 <assert_contents> 272 <assert_contents>
271 <is_valid_xml/> 273 <is_valid_xml/>
272 </assert_contents> 274 </assert_contents>
273 </output> 275 </output>
276 <assert_stdout>
277 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
278 </assert_stdout>
274 </test> 279 </test>
275 </tests> 280 </tests>
276 <help><![CDATA[Annotates MS/MS spectra using Mascot. 281 <help><![CDATA[Annotates MS/MS spectra using Mascot.
277 282
278 283
279 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MascotAdapter.html]]></help> 284 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MascotAdapter.html]]></help>
280 <expand macro="references"/> 285 <expand macro="references"/>
281 </tool> 286 </tool>