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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1
author galaxyp
date Mon, 15 Jul 2024 18:21:18 +0000
parents 01a572a3a716
children
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6:01a572a3a716 7:cf9a994e0447
1 <tool id="morpheus" name="Morpheus" version="2.255.0"> 1 <tool id="morpheus" name="Morpheus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>database search algorithm for high-resolution tandem mass spectra</description> 2 <description>database search algorithm for high-resolution tandem mass spectra</description>
3 <macros> 3 <macros>
4 <xml name="modification_options"> 4 <import>macros.xml</import>
5 <option value="acetylation of protein N-terminus">acetylation of protein N-terminus</option>
6 <option value="acetylation of lysine">acetylation of lysine</option>
7 <option value="phosphorylation of S">phosphorylation of S</option>
8 <option value="phosphorylation of T">phosphorylation of T</option>
9 <option value="phosphorylation of Y">phosphorylation of Y</option>
10 <option value="deamidation of N">deamidation of N</option>
11 <option value="deamidation of Q">deamidation of Q</option>
12 <option value="pyro-cmC">pyro-cmC</option>
13 <option value="pyro-E">pyro-E</option>
14 <option value="pyro-Q">pyro-Q</option>
15 <option value="TMT zero on peptide N-terminus">TMT zero on peptide N-terminus</option>
16 <option value="TMT zero on K">TMT zero on K</option>
17 <option value="TMT zero on Y">TMT zero on Y</option>
18 <option value="TMT duplex on peptide N-terminus">TMT duplex on peptide N-terminus</option>
19 <option value="TMT duplex on K">TMT duplex on K</option>
20 <option value="TMT duplex on Y">TMT duplex on Y</option>
21 <option value="TMT sixplex/tenplex on peptide N-terminus">TMT sixplex/tenplex on peptide N-terminus</option>
22 <option value="TMT sixplex/tenplex on K">TMT sixplex/tenplex on K</option>
23 <option value="TMT sixplex/tenplex on Y">TMT sixplex/tenplex on Y</option>
24 <option value="iTRAQ 4-plex on peptide N-terminus">iTRAQ 4-plex on peptide N-terminus</option>
25 <option value="iTRAQ 4-plex on K">iTRAQ 4-plex on K</option>
26 <option value="iTRAQ 4-plex on Y">iTRAQ 4-plex on Y</option>
27 <option value="iTRAQ 8-plex on peptide N-terminus">iTRAQ 8-plex on peptide N-terminus</option>
28 <option value="iTRAQ 8-plex on K">iTRAQ 8-plex on K</option>
29 <option value="iTRAQ 8-plex on Y ">iTRAQ 8-plex on Y </option>
30 </xml>
31 <xml name="variable_modification_options">
32 <option value="oxidation of M" selected="true">oxidation of M</option>
33 <option value="carbamidomethylation of C">carbamidomethylation of C</option>
34 <expand macro="modification_options"/>
35 </xml>
36 <xml name="fixed_modification_options">
37 <option value="carbamidomethylation of C" selected="true">carbamidomethylation of C</option>
38 <option value="oxidation of M">oxidation of M</option>
39 <expand macro="modification_options"/>
40 </xml>
41 </macros> 5 </macros>
42 6 <expand macro="edam_ontology"/>
43 <requirements> 7 <expand macro="biotools"/>
44 <requirement type="package" version="255">morpheus</requirement> 8 <expand macro="requirements"/>
45 </requirements>
46
47 <stdio> 9 <stdio>
48 <exit_code range="1:" /> 10 <exit_code range="1:" />
49 <regex match="System..*Exception" 11 <regex match="System..*Exception"
50 source="both" 12 source="both"
51 level="fatal" 13 level="fatal"
148 -fm="$fmods" 110 -fm="$fmods"
149 #end if 111 #end if
150 #if str($vm) != 'None': 112 #if str($vm) != 'None':
151 #set $vmods = str($vm).replace(',',';') 113 #set $vmods = str($vm).replace(',',';')
152 -vm="$vmods" 114 -vm="$vmods"
153 #end if 115 #end if
116 #if str($p) != 'None':
117 -p="$p"
118 #end if
154 -mt=\${GALAXY_SLOTS:-4} 119 -mt=\${GALAXY_SLOTS:-4}
155 #set $out_list = 'log.txt summary.tsv aggregate.PSMs.tsv aggregate.unique_peptides.tsv aggregate.protein_groups.tsv aggregate.mzid *.pep.xml' 120 #set $out_list = 'log.txt summary.tsv aggregate.PSMs.tsv aggregate.unique_peptides.tsv aggregate.protein_groups.tsv aggregate.mzid *.pep.xml'
156 #if len($input_list) == 1: 121 #if len($input_list) == 1:
157 && ln -s *.log.txt log.txt 122 && ln -s *.log.txt log.txt
158 && ln -s *.mzid aggregate.mzid 123 && ln -s *.mzid aggregate.mzid
169 <param name="fm" type="select" multiple="true" optional="true" label="Fixed Modifications"> 134 <param name="fm" type="select" multiple="true" optional="true" label="Fixed Modifications">
170 <expand macro="fixed_modification_options" /> 135 <expand macro="fixed_modification_options" />
171 </param> 136 </param>
172 <param name="vm" type="select" multiple="true" optional="true" label="Variable Modifications"> 137 <param name="vm" type="select" multiple="true" optional="true" label="Variable Modifications">
173 <expand macro="variable_modification_options" /> 138 <expand macro="variable_modification_options" />
174 </param> 139 </param>
140 <param name="p" type="select" label="Proteases">
141 <expand macro="proteases_options"/>
142 </param>
175 <param name="fdr" type="float" value="1" optional="true" min="0.0" max="100.0" label="FDR (Maximum False Discovery Rate percent)" /> 143 <param name="fdr" type="float" value="1" optional="true" min="0.0" max="100.0" label="FDR (Maximum False Discovery Rate percent)" />
176 <param name="mvmi" type="integer" value="1024" optional="true" min="0" label="Maximum Variable Modification Isoforms Per Peptide" /> 144 <param name="mvmi" type="integer" value="1024" optional="true" min="0" label="Maximum Variable Modification Isoforms Per Peptide" />
177 <param name="precmtv" type="float" value="10." optional="true" label="Precursor Mass Tolerance Value" /> 145 <param name="precmtv" type="float" value="10." optional="true" label="Precursor Mass Tolerance Value" />
178 <param name="precmtu" type="select" optional="true" label="Precursor Mass Tolerance Units"> 146 <param name="precmtu" type="select" optional="true" label="Precursor Mass Tolerance Units">
179 <option value="ppm" selected="true">ppm</option> 147 <option value="ppm" selected="true">ppm</option>
268 <assert_contents> 236 <assert_contents>
269 <has_text text="K.VETYM(oxidation of M)ETK.I" /> 237 <has_text text="K.VETYM(oxidation of M)ETK.I" />
270 <not_has_text text="K.TTGSSSSSSSK.K" /> 238 <not_has_text text="K.TTGSSSSSSSK.K" />
271 </assert_contents> 239 </assert_contents>
272 </output> 240 </output>
241 </test>
242 <test>
243 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
244 <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/>
245 <param name="fdr" value="1"/>
246 <param name="mvmi" value="1024"/>
247 <param name="precmt" value="Monoisotopic"/>
248 <param name="precmtu" value="Da"/>
249 <param name="precmtv" value="2.5"/>
250 <param name="fm" value="carbamidomethylation of C"/>
251 <param name="vm" value="oxidation of M"/>
252 <param name="p" value="trypsin" />
253 <output name="output_psms">
254 <assert_contents>
255 <has_text text="K.DGM(oxidation of M)KAYAQNVQQR.E" />
256 <not_has_text text="K.TTGSSSSSSSK.K" />
257 </assert_contents>
258 </output>
273 </test> 259 </test>
274 <test> 260 <test>
275 <param name="inputs" value="test_input.mzML" ftype="mzml"/> 261 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
276 <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/> 262 <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>
277 <param name="fdr" value="1"/> 263 <param name="fdr" value="1"/>
281 <param name="precmtv" value="2.5"/> 267 <param name="precmtv" value="2.5"/>
282 <param name="fm" value="carbamidomethylation of C"/> 268 <param name="fm" value="carbamidomethylation of C"/>
283 <param name="vm" value="oxidation of M"/> 269 <param name="vm" value="oxidation of M"/>
284 <output name="output_psms"> 270 <output name="output_psms">
285 <assert_contents> 271 <assert_contents>
286 <has_text text="R.KRSLFDS(UniProt: Phosphoserine)AFSSR.A" /> 272 <has_text text="K.RSPSGNISTNSMR.P" />
287 <not_has_text text="K.KYFLENKIGTDR.R" /> 273 <not_has_text text="K.KYFLENKIGTDR.R" />
288 </assert_contents> 274 </assert_contents>
289 </output> 275 </output>
290 </test> 276 </test>
291 <test> 277 <test>
305 <has_text text="K.KTLKSDGVAGLYR.G" /> 291 <has_text text="K.KTLKSDGVAGLYR.G" />
306 <not_has_text text="K.RSPSGNISTNSMR.P" /> 292 <not_has_text text="K.RSPSGNISTNSMR.P" />
307 </assert_contents> 293 </assert_contents>
308 </output> 294 </output>
309 </test> 295 </test>
310 296 <test>
297 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
298 <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>
299 <param name="fdr" value="1"/>
300 <param name="mvmi" value="1024"/>
301 <param name="precmt" value="Monoisotopic"/>
302 <param name="precmtu" value="Da"/>
303 <param name="precmtv" value="2.5"/>
304 <param name="fm" value="carbamidomethylation of C"/>
305 <param name="vm" value="oxidation of M"/>
306 <param name="p" value="trypsin"/>
307 <param name="adv_options_selector" value="set"/>
308 <param name="prodmtv" value=".01"/>
309 <output name="output_psms">
310 <assert_contents>
311 <has_text text="K.KTLKSDGVAGLYR.G" />
312 <not_has_text text="K.KYFLENKIGTDR.R" />
313 </assert_contents>
314 </output>
315 </test>
311 </tests> 316 </tests>
312 <help><![CDATA[ 317 <help><![CDATA[
313 Morpheus_ is a database search algorithm for high-resolution tandem mass spectra. 318 Morpheus_ is a database search algorithm for high-resolution tandem mass spectra.
314 319
315 When a Uniprot Proteome XML file is used for the search database, Morpheus will include all known modifications from the proteome in searching for peptide spectral matches. To fetch Uniprot Proteome XML files see: http://www.uniprot.org/help/retrieve_sets 320 When a Uniprot Proteome XML file is used for the search database, Morpheus will include all known modifications from the proteome in searching for peptide spectral matches. To fetch Uniprot Proteome XML files see: http://www.uniprot.org/help/retrieve_sets