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comparison MascotAdapter.xml @ 0:ec7b8772f4c9 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:35:50 -0500
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children 36da1e3613ea
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-1:000000000000 0:ec7b8772f4c9
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 CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="MascotAdapter" name="MascotAdapter" version="2.1.0">
5 <description>Annotates MS/MS spectra using Mascot.</description>
6 <macros>
7 <token name="@EXECUTABLE@">MascotAdapter</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>MascotAdapter
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_mascot_in:
22 -mascot_in
23 #end if
24 #if $param_mascot_out:
25 -mascot_out
26 #end if
27 #if $param_instrument:
28 -instrument "$param_instrument"
29 #end if
30 #if $param_precursor_mass_tolerance:
31 -precursor_mass_tolerance $param_precursor_mass_tolerance
32 #end if
33 #if $param_peak_mass_tolerance:
34 -peak_mass_tolerance $param_peak_mass_tolerance
35 #end if
36 #if $param_taxonomy:
37 -taxonomy $param_taxonomy
38 #end if
39
40 #if $rep_param_modifications:
41 -modifications
42 #for token in $rep_param_modifications:
43 #if " " in str(token):
44 "$token.param_modifications"
45 #else
46 $token.param_modifications
47 #end if
48 #end for
49 #end if
50
51 #if $rep_param_variable_modifications:
52 -variable_modifications
53 #for token in $rep_param_variable_modifications:
54 #if " " in str(token):
55 "$token.param_variable_modifications"
56 #else
57 $token.param_variable_modifications
58 #end if
59 #end for
60 #end if
61
62 #if $rep_param_charges:
63 -charges
64 #for token in $rep_param_charges:
65 #if " " in str(token):
66 "$token.param_charges"
67 #else
68 $token.param_charges
69 #end if
70 #end for
71 #end if
72 #if $param_db:
73 -db "$param_db"
74 #end if
75 #if $param_hits:
76 -hits "$param_hits"
77 #end if
78 #if $param_cleavage:
79 -cleavage $param_cleavage
80 #end if
81 #if $param_missed_cleavages:
82 -missed_cleavages $param_missed_cleavages
83 #end if
84 #if $param_sig_threshold:
85 -sig_threshold $param_sig_threshold
86 #end if
87 #if $param_pep_homol:
88 -pep_homol $param_pep_homol
89 #end if
90 #if $param_pep_ident:
91 -pep_ident $param_pep_ident
92 #end if
93 #if $param_pep_rank:
94 -pep_rank $param_pep_rank
95 #end if
96 #if $param_prot_score:
97 -prot_score $param_prot_score
98 #end if
99 #if $param_pep_score:
100 -pep_score $param_pep_score
101 #end if
102 #if $param_pep_exp_z:
103 -pep_exp_z $param_pep_exp_z
104 #end if
105 #if $param_show_unassigned:
106 -show_unassigned $param_show_unassigned
107 #end if
108 #if $param_first_dim_rt:
109 -first_dim_rt $param_first_dim_rt
110 #end if
111 #if $param_boundary:
112 -boundary "$param_boundary"
113 #end if
114 #if $param_mass_type:
115 -mass_type $param_mass_type
116 #end if
117 #if $param_mascot_directory:
118 -mascot_directory "$param_mascot_directory"
119 #end if
120 #if $param_temp_data_directory:
121 -temp_data_directory "$param_temp_data_directory"
122 #end if
123 #if $adv_opts.adv_opts_selector=='advanced':
124 #if $adv_opts.param_force:
125 -force
126 #end if
127 #end if
128 </command>
129 <inputs>
130 <param name="param_in" type="data" format="text" label="input file in mzData format" help="(-in) &lt;br&gt;Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read"/>
131 <param name="param_mascot_in" display="radio" type="boolean" truevalue="-mascot_in" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in mzData and write Mascot generic format" help="(-mascot_in) "/>
132 <param name="param_mascot_out" display="radio" type="boolean" truevalue="-mascot_out" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in a Mascot results file (.mascotXML) and write idXML" help="(-mascot_out) "/>
133 <param name="param_instrument" type="text" size="30" value="Default" label="the instrument that was used to measure the spectra" help="(-instrument) ">
134 <sanitizer>
135 <valid initial="string.printable">
136 <remove value="'"/>
137 <remove value="&quot;"/>
138 </valid>
139 </sanitizer>
140 </param>
141 <param name="param_precursor_mass_tolerance" type="float" value="2.0" label="the precursor mass tolerance" help="(-precursor_mass_tolerance) "/>
142 <param name="param_peak_mass_tolerance" type="float" value="1.0" label="the peak mass tolerance" help="(-peak_mass_tolerance) "/>
143 <param name="param_taxonomy" type="select" optional="False" value="All entries" label="the taxonomy" help="(-taxonomy) ">
144 <option value="All entries" selected="true">All entries</option>
145 <option value=". . Archaea (Archaeobacteria)">. . Archaea (Archaeobacteria)</option>
146 <option value=". . Eukaryota (eucaryotes)">. . Eukaryota (eucaryotes)</option>
147 <option value=". . . . Alveolata (alveolates)">. . . . Alveolata (alveolates)</option>
148 <option value=". . . . . . Plasmodium falciparum (malaria parasite)">. . . . . . Plasmodium falciparum (malaria parasite)</option>
149 <option value=". . . . . . Other Alveolata">. . . . . . Other Alveolata</option>
150 <option value=". . . . Metazoa (Animals)">. . . . Metazoa (Animals)</option>
151 <option value=". . . . . . Caenorhabditis elegans">. . . . . . Caenorhabditis elegans</option>
152 <option value=". . . . . . Drosophila (fruit flies)">. . . . . . Drosophila (fruit flies)</option>
153 <option value=". . . . . . Chordata (vertebrates and relatives)">. . . . . . Chordata (vertebrates and relatives)</option>
154 <option value=". . . . . . . . bony vertebrates">. . . . . . . . bony vertebrates</option>
155 <option value=". . . . . . . . . . lobe-finned fish and tetrapod clade">. . . . . . . . . . lobe-finned fish and tetrapod clade</option>
156 <option value=". . . . . . . . . . . . Mammalia (mammals)">. . . . . . . . . . . . Mammalia (mammals)</option>
157 <option value=". . . . . . . . . . . . . . Primates">. . . . . . . . . . . . . . Primates</option>
158 <option value=". . . . . . . . . . . . . . . . Homo sapiens (human)">. . . . . . . . . . . . . . . . Homo sapiens (human)</option>
159 <option value=". . . . . . . . . . . . . . . . Other primates">. . . . . . . . . . . . . . . . Other primates</option>
160 <option value=". . . . . . . . . . . . . . Rodentia (Rodents)">. . . . . . . . . . . . . . Rodentia (Rodents)</option>
161 <option value=". . . . . . . . . . . . . . . . Mus.">. . . . . . . . . . . . . . . . Mus.</option>
162 <option value=". . . . . . . . . . . . . . . . . . Mus musculus (house mouse)">. . . . . . . . . . . . . . . . . . Mus musculus (house mouse)</option>
163 <option value=". . . . . . . . . . . . . . . . Rattus">. . . . . . . . . . . . . . . . Rattus</option>
164 <option value=". . . . . . . . . . . . . . . . Other rodentia">. . . . . . . . . . . . . . . . Other rodentia</option>
165 <option value=". . . . . . . . . . . . . . Other mammalia">. . . . . . . . . . . . . . Other mammalia</option>
166 <option value=". . . . . . . . . . . . Xenopus laevis (African clawed frog)">. . . . . . . . . . . . Xenopus laevis (African clawed frog)</option>
167 <option value=". . . . . . . . . . . . Other lobe-finned fish and tetrapod clade">. . . . . . . . . . . . Other lobe-finned fish and tetrapod clade</option>
168 <option value=". . . . . . . . . . Actinopterygii (ray-finned fishes)">. . . . . . . . . . Actinopterygii (ray-finned fishes)</option>
169 <option value=". . . . . . . . . . . . Takifugu rubripes (Japanese Pufferfish)">. . . . . . . . . . . . Takifugu rubripes (Japanese Pufferfish)</option>
170 <option value=". . . . . . . . . . . . Danio rerio (zebra fish)">. . . . . . . . . . . . Danio rerio (zebra fish)</option>
171 <option value=". . . . . . . . . . . . Other Actinopterygii">. . . . . . . . . . . . Other Actinopterygii</option>
172 <option value=". . . . . . . . Other Chordata">. . . . . . . . Other Chordata</option>
173 <option value=". . . . . . Other Metazoa">. . . . . . Other Metazoa</option>
174 <option value=". . . . Dictyostelium discoideum">. . . . Dictyostelium discoideum</option>
175 <option value=". . . . Fungi">. . . . Fungi</option>
176 <option value=". . . . . . Saccharomyces Cerevisiae (baker's yeast)">. . . . . . Saccharomyces Cerevisiae (baker's yeast)</option>
177 <option value=". . . . . . Schizosaccharomyces pombe (fission yeast)">. . . . . . Schizosaccharomyces pombe (fission yeast)</option>
178 <option value=". . . . . . Pneumocystis carinii">. . . . . . Pneumocystis carinii</option>
179 <option value=". . . . . . Other Fungi">. . . . . . Other Fungi</option>
180 <option value=". . . . Viridiplantae (Green Plants)">. . . . Viridiplantae (Green Plants)</option>
181 <option value=". . . . . . Arabidopsis thaliana (thale cress)">. . . . . . Arabidopsis thaliana (thale cress)</option>
182 <option value=". . . . . . Oryza sativa (rice)">. . . . . . Oryza sativa (rice)</option>
183 <option value=". . . . . . Other green plants">. . . . . . Other green plants</option>
184 <option value=". . . . Other Eukaryota">. . . . Other Eukaryota</option>
185 <option value=". . Bacteria (Eubacteria)">. . Bacteria (Eubacteria)</option>
186 <option value=". . . . Actinobacteria (class)">. . . . Actinobacteria (class)</option>
187 <option value=". . . . . . Mycobacterium tuberculosis complex">. . . . . . Mycobacterium tuberculosis complex</option>
188 <option value=". . . . . . Other Actinobacteria (class)">. . . . . . Other Actinobacteria (class)</option>
189 <option value=". . . . Firmicutes (gram-positive bacteria)">. . . . Firmicutes (gram-positive bacteria)</option>
190 <option value=". . . . . . Bacillus subtilis">. . . . . . Bacillus subtilis</option>
191 <option value=". . . . . . Mycoplasma">. . . . . . Mycoplasma</option>
192 <option value=". . . . . . Streptococcus Pneumoniae">. . . . . . Streptococcus Pneumoniae</option>
193 <option value=". . . . . . Streptomyces coelicolor">. . . . . . Streptomyces coelicolor</option>
194 <option value=". . . . . . Other Firmicutes">. . . . . . Other Firmicutes</option>
195 <option value=". . . . Proteobacteria (purple bacteria)">. . . . Proteobacteria (purple bacteria)</option>
196 <option value=". . . . . . Agrobacterium tumefaciens">. . . . . . Agrobacterium tumefaciens</option>
197 <option value=". . . . . . Campylobacter jejuni">. . . . . . Campylobacter jejuni</option>
198 <option value=". . . . . . Escherichia coli">. . . . . . Escherichia coli</option>
199 <option value=". . . . . . Neisseria meningitidis">. . . . . . Neisseria meningitidis</option>
200 <option value=". . . . . . Salmonella">. . . . . . Salmonella</option>
201 <option value=". . . . . . Other Proteobacteria">. . . . . . Other Proteobacteria</option>
202 <option value=". . . . Other Bacteria">. . . . Other Bacteria</option>
203 <option value=". . Viruses">. . Viruses</option>
204 <option value=". . . . Hepatitis C virus">. . . . Hepatitis C virus</option>
205 <option value=". . . . Other viruses">. . . . Other viruses</option>
206 <option value=". . Other (includes plasmids and artificial sequences)">. . Other (includes plasmids and artificial sequences)</option>
207 <option value=". . unclassified">. . unclassified</option>
208 <option value=". . Species information unavailable">. . Species information unavailable</option>
209 </param>
210 <repeat name="rep_param_modifications" min="0" max="1" title="param_modifications">
211 <param name="param_modifications" type="text" size="30" label="the modifications i.e. Carboxymethyl (C)" help="(-modifications) ">
212 <sanitizer>
213 <valid initial="string.printable">
214 <remove value="'"/>
215 <remove value="&quot;"/>
216 </valid>
217 </sanitizer>
218 </param>
219 </repeat>
220 <repeat name="rep_param_variable_modifications" min="0" max="1" title="param_variable_modifications">
221 <param name="param_variable_modifications" type="text" size="30" label="the variable modifications i.e. Carboxymethyl (C)" help="(-variable_modifications) ">
222 <sanitizer>
223 <valid initial="string.printable">
224 <remove value="'"/>
225 <remove value="&quot;"/>
226 </valid>
227 </sanitizer>
228 </param>
229 </repeat>
230 <repeat name="rep_param_charges" min="0" max="1" title="param_charges">
231 <param name="param_charges" type="text" size="30" value="1+ 2+ 3+" label="the different charge states" help="(-charges) ">
232 <sanitizer>
233 <valid initial="string.printable">
234 <remove value="'"/>
235 <remove value="&quot;"/>
236 </valid>
237 </sanitizer>
238 </param>
239 </repeat>
240 <param name="param_db" type="text" size="30" value="MSDB" label="the database to search in" help="(-db) ">
241 <sanitizer>
242 <valid initial="string.printable">
243 <remove value="'"/>
244 <remove value="&quot;"/>
245 </valid>
246 </sanitizer>
247 </param>
248 <param name="param_hits" type="text" size="30" value="AUTO" label="the number of hits to report" help="(-hits) ">
249 <sanitizer>
250 <valid initial="string.printable">
251 <remove value="'"/>
252 <remove value="&quot;"/>
253 </valid>
254 </sanitizer>
255 </param>
256 <param name="param_cleavage" type="select" optional="False" value="Trypsin" label="The enzyme descriptor to the enzyme used for digestion" help="(-cleavage) (Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)">
257 <option value="Trypsin" selected="true">Trypsin</option>
258 <option value="Arg-C">Arg-C</option>
259 <option value="Asp-N">Asp-N</option>
260 <option value="Asp-N_ambic">Asp-N_ambic</option>
261 <option value="Chymotrypsin">Chymotrypsin</option>
262 <option value="CNBr">CNBr</option>
263 <option value="CNBr+Trypsin">CNBr+Trypsin</option>
264 <option value="Formic_acid">Formic_acid</option>
265 <option value="Lys-C">Lys-C</option>
266 <option value="Lys-C/P">Lys-C/P</option>
267 <option value="PepsinA">PepsinA</option>
268 <option value="Tryp-CNBr">Tryp-CNBr</option>
269 <option value="TrypChymo">TrypChymo</option>
270 <option value="Trypsin/P">Trypsin/P</option>
271 <option value="V8-DE">V8-DE</option>
272 <option value="V8-E">V8-E</option>
273 <option value="semiTrypsin">semiTrypsin</option>
274 <option value="LysC+AspN">LysC+AspN</option>
275 <option value="None">None</option>
276 </param>
277 <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="0" label="number of allowed missed cleavages" help="(-missed_cleavages) "/>
278 <param name="param_sig_threshold" type="float" value="0.05" label="significance threshold" help="(-sig_threshold) "/>
279 <param name="param_pep_homol" type="float" value="1.0" label="peptide homology threshold" help="(-pep_homol) "/>
280 <param name="param_pep_ident" type="float" value="1.0" label="peptide ident threshold" help="(-pep_ident) "/>
281 <param name="param_pep_rank" type="integer" value="1" label="peptide rank" help="(-pep_rank) "/>
282 <param name="param_prot_score" type="float" value="1.0" label="protein score" help="(-prot_score) "/>
283 <param name="param_pep_score" type="float" value="1.0" label="peptide score" help="(-pep_score) "/>
284 <param name="param_pep_exp_z" type="integer" value="1" label="peptide expected charge" help="(-pep_exp_z) "/>
285 <param name="param_show_unassigned" type="integer" value="1" label="show_unassigned" help="(-show_unassigned) "/>
286 <param name="param_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="(-first_dim_rt) "/>
287 <param name="param_boundary" type="text" size="30" label="MIME boundary for mascot output format" help="(-boundary) ">
288 <sanitizer>
289 <valid initial="string.printable">
290 <remove value="'"/>
291 <remove value="&quot;"/>
292 </valid>
293 </sanitizer>
294 </param>
295 <param name="param_mass_type" display="radio" type="select" optional="False" value="Monoisotopic" label="mass type" help="(-mass_type) ">
296 <option value="Monoisotopic" selected="true">Monoisotopic</option>
297 <option value="Average">Average</option>
298 </param>
299 <param name="param_mascot_directory" type="text" size="30" label="the directory in which mascot is located" help="(-mascot_directory) ">
300 <sanitizer>
301 <valid initial="string.printable">
302 <remove value="'"/>
303 <remove value="&quot;"/>
304 </valid>
305 </sanitizer>
306 </param>
307 <param name="param_temp_data_directory" type="text" size="30" label="a directory in which some temporary files can be stored" help="(-temp_data_directory) ">
308 <sanitizer>
309 <valid initial="string.printable">
310 <remove value="'"/>
311 <remove value="&quot;"/>
312 </valid>
313 </sanitizer>
314 </param>
315 <expand macro="advanced_options">
316 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
317 </expand>
318 </inputs>
319 <outputs>
320 <data name="param_out" format="data"/>
321 </outputs>
322 <help>Annotates MS/MS spectra using Mascot.
323
324
325 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MascotAdapter.html</help>
326 </tool>