Mercurial > repos > galaxyp > peptideshaker
comparison searchgui.xml @ 20:2cafc729b2ae draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
| author | iracooke |
|---|---|
| date | Sun, 31 May 2015 09:05:57 -0400 |
| parents | |
| children | dfaea053e32f |
comparison
equal
deleted
inserted
replaced
| 19:7e61179c5952 | 20:2cafc729b2ae |
|---|---|
| 1 <tool id="search_gui" name="Search GUI" version="1.27.0"> | |
| 2 <description> | |
| 3 Perform protein identification using various search engines and prepare results for input to Peptide Shaker | |
| 4 </description> | |
| 5 <requirements> | |
| 6 <requirement type="package" version="1.27">searchgui</requirement> | |
| 7 </requirements> | |
| 8 <macros> | |
| 9 <import>macros.xml</import> | |
| 10 </macros> | |
| 11 <expand macro="stdio" /> | |
| 12 <command> | |
| 13 <![CDATA[ | |
| 14 #from datetime import datetime | |
| 15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") | |
| 16 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s") | |
| 17 #set $temp_stderr = "searchgui_stderr" | |
| 18 | |
| 19 mkdir output; | |
| 20 mkdir output_reports; | |
| 21 cwd=`pwd`; | |
| 22 #for $mgf in $peak_lists: | |
| 23 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" | |
| 24 ln -s -f '${mgf}' '${input_name}'; | |
| 25 #end for | |
| 26 ##ln -s "${input_database}" input_database.fasta; | |
| 27 cp "${input_database}" input_database.fasta; | |
| 28 | |
| 29 ########################################### | |
| 30 #### Creating decoy database #### | |
| 31 ########################################### | |
| 32 #if $create_decoy: | |
| 33 echo "Creating decoy database."; | |
| 34 java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy && | |
| 35 rm input_database.fasta && | |
| 36 cp input_database_concatenated_target_decoy.fasta input_database.fasta && | |
| 37 ##ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; | |
| 38 #end if | |
| 39 | |
| 40 ##################################################### | |
| 41 ## generate IdentificationParameters for SearchGUI ## | |
| 42 ##################################################### | |
| 43 | |
| 44 (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI | |
| 45 -out SEARCHGUI_IdentificationParameters.parameters | |
| 46 | |
| 47 @GENERAL_PARAMETERS@ | |
| 48 | |
| 49 -db input_database.fasta | |
| 50 | |
| 51 #if $advanced.advanced_type_selector == "advanced": | |
| 52 | |
| 53 #if $advanced.xtandem.xtandem_selector == "yes" | |
| 54 | |
| 55 -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks} | |
| 56 -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks} | |
| 57 -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz} | |
| 58 -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass} | |
| 59 -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr} | |
| 60 | |
| 61 #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes" | |
| 62 -xtandem_refine 1 | |
| 63 -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc} | |
| 64 -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_semi} | |
| 65 -xtandem_refine_p_mut ${advanced.xtandem.xtandem_refine.xtandem_refine_p_mut} | |
| 66 -xtandem_refine_snaps ${advanced.xtandem.xtandem_refine.xtandem_refine_snaps} | |
| 67 -xtandem_refine_spec_synt ${advanced.xtandem.xtandem_refine.xtandem_refine_spec_synt} | |
| 68 #end if | |
| 69 #end if | |
| 70 | |
| 71 #if $advanced.omssa.omssa_selector == "yes" | |
| 72 -omssa_hitlist_length ${advanced.omssa.hitlist_length} | |
| 73 -omssa_remove_prec ${advanced.omssa.remove_precursor} | |
| 74 -omssa_scale_prec ${advanced.omssa.scale_precursor} | |
| 75 -omssa_estimate_charge ${advanced.omssa.estimate_charge} | |
| 76 #end if | |
| 77 | |
| 78 #if $advanced.msgf.msgf_selector == "yes" | |
| 79 -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length} | |
| 80 -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length} | |
| 81 -msgf_termini ${advanced.msgf.msgf_termini} | |
| 82 -msgf_num_ptms ${advanced.msgf.msgf_num_ptms} | |
| 83 #end if | |
| 84 | |
| 85 ##if $advanced.ms_amanda.ms_amanda_selector == "yes" | |
| 86 ##end if | |
| 87 | |
| 88 #end if | |
| 89 | |
| 90 2> $temp_stderr) | |
| 91 && | |
| 92 | |
| 93 ################ | |
| 94 ## Search CLI ## | |
| 95 ################ | |
| 96 (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI | |
| 97 -temp_folder `pwd` | |
| 98 -spectrum_files \$cwd | |
| 99 -output_folder \$cwd/output | |
| 100 -id_params SEARCHGUI_IdentificationParameters.parameters | |
| 101 | |
| 102 -threads "\${GALAXY_SLOTS:-12}" | |
| 103 -correct_titles "${correct_titles}" | |
| 104 $missing_titles | |
| 105 -mgf_splitting "${mgf_splitting}" | |
| 106 -mgf_spectrum_count "${mgf_spectrum_count}" | |
| 107 | |
| 108 ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created | |
| 109 ## the tree is generated afterwards in PeptideShaker | |
| 110 -protein_index 0 | |
| 111 | |
| 112 ##-makeblastdb_folder \$BLAST_ROOT_DIR | |
| 113 | |
| 114 #if $advanced.advanced_type_selector == "advanced": | |
| 115 | |
| 116 #if $advanced.xtandem.xtandem_selector == "yes" | |
| 117 -xtandem 1 | |
| 118 #else | |
| 119 -xtandem 0 | |
| 120 #end if | |
| 121 | |
| 122 #if $advanced.omssa.omssa_selector == "yes" | |
| 123 -omssa 1 | |
| 124 #else | |
| 125 -omssa 0 | |
| 126 #end if | |
| 127 | |
| 128 #if $advanced.msgf.msgf_selector == "yes" | |
| 129 -msgf 1 | |
| 130 #else | |
| 131 -msgf 0 | |
| 132 #end if | |
| 133 | |
| 134 #if $advanced.myrimatch.myrimatch_selector == "yes" | |
| 135 -myrimatch 1 | |
| 136 #else | |
| 137 -myrimatch 0 | |
| 138 #end if | |
| 139 | |
| 140 #if $advanced.comet.comet_selector == "yes" | |
| 141 -comet 1 | |
| 142 #else | |
| 143 -comet 0 | |
| 144 #end if | |
| 145 | |
| 146 #if $advanced.ms_amanda.ms_amanda_selector == "yes" | |
| 147 -ms_amanda 1 | |
| 148 #else | |
| 149 -ms_amanda 0 | |
| 150 #end if | |
| 151 | |
| 152 #if $advanced.tide.tide_selector == "yes" | |
| 153 -tide 1 | |
| 154 #else | |
| 155 -tide 0 | |
| 156 #end if | |
| 157 | |
| 158 #else | |
| 159 -ms_amanda 0 -tide 0 | |
| 160 #end if | |
| 161 | |
| 162 ## single zip file | |
| 163 -output_option 0 | |
| 164 | |
| 165 ## mgf and database in output | |
| 166 -output_data 1 | |
| 167 | |
| 168 2>> $temp_stderr) | |
| 169 | |
| 170 && | |
| 171 | |
| 172 (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr) | |
| 173 | |
| 174 && | |
| 175 | |
| 176 exit_code_for_galaxy=\$?; | |
| 177 cat $temp_stderr 2>&1; | |
| 178 (exit \$exit_code_for_galaxy) | |
| 179 ]]> | |
| 180 </command> | |
| 181 <inputs> | |
| 182 <param format="fasta" name="input_database" type="data" label="Protein Database" | |
| 183 help="Select FASTA database from history"/> | |
| 184 | |
| 185 <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true" | |
| 186 label="Create a concatenated target/decoy database before running PeptideShaker" | |
| 187 help="Selecting this option will help PeptideShaker calculate FDR values" /> | |
| 188 | |
| 189 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)" | |
| 190 help="Select appropriate MGF dataset(s) from history" /> | |
| 191 | |
| 192 <expand macro="general_options"/> | |
| 193 | |
| 194 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?" | |
| 195 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option"> | |
| 196 <option value="0">no correction</option> | |
| 197 <option value="1" selected="True">rename spectra</option> | |
| 198 <option value="2">delete spectra</option> | |
| 199 </param> | |
| 200 | |
| 201 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" | |
| 202 label="Add missing spectrum titles" help="(-missing_titles)"/> | |
| 203 | |
| 204 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf" | |
| 205 help="Choose a smaller value if you are running on a machine with limited memory"/> | |
| 206 | |
| 207 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" | |
| 208 help="Choose a smaller value if you are running on a machine with limited memory"/> | |
| 209 | |
| 210 <conditional name="advanced"> | |
| 211 <param name="advanced_type_selector" type="select" label="Basic or Advanced Search options"> | |
| 212 <option value="basic" selected="True">Basic</option> | |
| 213 <option value="advanced">Advanced</option> | |
| 214 </param> | |
| 215 <when value="basic" /> | |
| 216 <when value="advanced"> | |
| 217 <conditional name="xtandem"> | |
| 218 <param name="xtandem_selector" type="select" label="Run X!Tandem search"> | |
| 219 <option value="yes" selected="True">Search with X!Tandem</option> | |
| 220 <option value="no">No X!Tandem search</option> | |
| 221 </param> | |
| 222 <when value="no" /> | |
| 223 <when value="yes"> | |
| 224 <param name="xtandem_npeaks" type="integer" value="50" | |
| 225 label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/> | |
| 226 <param name="xtandem_min_peaks" type="integer" value="15" | |
| 227 label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/> | |
| 228 <param name="xtandem_min_frag_mz" type="integer" value="200" | |
| 229 label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/> | |
| 230 <param name="xtandem_min_prec_mass" type="integer" value="200" | |
| 231 label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/> | |
| 232 <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0" | |
| 233 label="X!Tandem: Noise Suppression" help="Use noise suppression"/> | |
| 234 | |
| 235 <conditional name="xtandem_refine"><!-- -xtandem_refine --> | |
| 236 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement"> | |
| 237 <option value="no" selected="True">Don't refine</option> | |
| 238 <option value="yes" >Use refinement</option> | |
| 239 </param> | |
| 240 <when value="no"/> | |
| 241 <when value="yes"> | |
| 242 <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" | |
| 243 label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/> | |
| 244 <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" | |
| 245 label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/> | |
| 246 <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" | |
| 247 label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/> | |
| 248 <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" | |
| 249 label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/> | |
| 250 <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" | |
| 251 label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/> | |
| 252 </when> | |
| 253 </conditional> | |
| 254 </when> | |
| 255 </conditional> | |
| 256 | |
| 257 <conditional name="omssa"> | |
| 258 <param name="omssa_selector" type="select" label="Run OMSSA search"> | |
| 259 <option value="yes" selected="True">Search with OMSSA</option> | |
| 260 <option value="no">No OMSSA search</option> | |
| 261 </param> | |
| 262 <when value="no" /> | |
| 263 <when value="yes"> | |
| 264 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" /> | |
| 265 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/> | |
| 266 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/> | |
| 267 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" /> | |
| 268 </when> | |
| 269 </conditional> | |
| 270 | |
| 271 <conditional name="msgf"> | |
| 272 <param name="msgf_selector" type="select" label="Run MSGF search"> | |
| 273 <option value="yes" selected="True">Search with MSGF</option> | |
| 274 <option value="no">No MSGF search</option> | |
| 275 </param> | |
| 276 <when value="no" /> | |
| 277 <when value="yes"> | |
| 278 <param name="msgf_min_pep_length" type="integer" value="6" | |
| 279 label="Minimum Peptide Length" help="Minimum length for a peptide to be considered"/> | |
| 280 <param name="msgf_max_pep_length" type="integer" value="30" | |
| 281 label="Maximum Peptide Length" help="Maximum length for a peptide to be considered"/> | |
| 282 <param name="msgf_termini" type="select" format="text" | |
| 283 label="Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2"> | |
| 284 <option value="0">0 (ie non-specific cleavage)</option> | |
| 285 <option value="1">1 (ie semi-tryptic cleavage)</option> | |
| 286 <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option> | |
| 287 </param> | |
| 288 <param name="msgf_num_ptms" label="Max PTMs per peptide" type="integer" value="2"/> | |
| 289 </when> | |
| 290 </conditional> | |
| 291 | |
| 292 <conditional name="myrimatch"> | |
| 293 <param name="myrimatch_selector" type="select" label="Run MyriMatch search"> | |
| 294 <option value="yes" selected="True">Search with MyriMatch</option> | |
| 295 <option value="no">No MyriMatch search</option> | |
| 296 </param> | |
| 297 <when value="no" /> | |
| 298 <when value="yes"> | |
| 299 </when> | |
| 300 </conditional> | |
| 301 | |
| 302 <conditional name="comet"> | |
| 303 <param name="comet_selector" type="select" label="Run Comet search"> | |
| 304 <option value="yes" selected="True">Search with Comet</option> | |
| 305 <option value="no">No Comet search</option> | |
| 306 </param> | |
| 307 <when value="no" /> | |
| 308 <when value="yes"> | |
| 309 </when> | |
| 310 </conditional> | |
| 311 | |
| 312 <conditional name="ms_amanda"> | |
| 313 <param name="ms_amanda_selector" type="select" label="Run MS Amanda search"> | |
| 314 <option value="yes">Search with MS Amanda</option> | |
| 315 <option value="no" selected="True">No MS Amanda search</option> | |
| 316 </param> | |
| 317 <when value="no" /> | |
| 318 <when value="yes"> | |
| 319 </when> | |
| 320 </conditional> | |
| 321 | |
| 322 <conditional name="tide"> | |
| 323 <param name="tide_selector" type="select" label="Run Tide search"> | |
| 324 <option value="yes">Search with Tide</option> | |
| 325 <option value="no" selected="True">No Comet search</option> | |
| 326 </param> | |
| 327 <when value="no" /> | |
| 328 <when value="yes"> | |
| 329 </when> | |
| 330 </conditional> | |
| 331 | |
| 332 </when> | |
| 333 </conditional> | |
| 334 </inputs> | |
| 335 <outputs> | |
| 336 <data name="searchgui_results" format="searchgui_zip" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> | |
| 337 </outputs> | |
| 338 <tests> | |
| 339 <test> | |
| 340 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> | |
| 341 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> | |
| 342 <param name="precursor_ion_tol" value="100"/> | |
| 343 <param name="fixed_modifications" value="carbamidomethyl c"/> | |
| 344 <param name="variable_modifications" value="oxidation of m"/> | |
| 345 <param name="min_charge" value="1"/> | |
| 346 <param name="max_charge" value="3"/> | |
| 347 <param name="advanced_type_selector" value="advanced"/> | |
| 348 <param name="xtandem_selector" value="yes"/> | |
| 349 <param name="xtandem_selector.xtandem_refine_selector" value="yes"/> | |
| 350 <param name="omssa_selector" value="no"/> | |
| 351 <param name="msgf_selector" value="yes"/> | |
| 352 <param name="ms_amanda_selector" value="no"/> | |
| 353 <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_zip" compare="sim_size" delta="600" /> | |
| 354 </test> | |
| 355 </tests> | |
| 356 <help> | |
| 357 **What it does** | |
| 358 | |
| 359 Runs multiple search engines on any number of MGF peak lists using the SearchGUI. | |
| 360 | |
| 361 By default X! Tandem, OMSSA, MS-GF+, Myrimatch and Comet are run. Optionally, Amanda and Tide engines can also be run. | |
| 362 | |
| 363 </help> | |
| 364 <expand macro="citations" /> | |
| 365 </tool> |