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comparison searchgui.xml @ 30:ad60446b1e93 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
author galaxyp
date Fri, 13 Jan 2017 14:15:42 -0500
parents 432140bcc7fe
children f3f67aa3123b
comparison
equal deleted inserted replaced
29:78fad25eff17 30:ad60446b1e93
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <requirements> 8 <requirements>
9 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> 9 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
10 <environment_variable name="LC_ALL" action="set_to">C</environment_variable>
11 </requirements> 10 </requirements>
12 <expand macro="stdio" /> 11 <expand macro="stdio" />
13 <command> 12 <command>
14 <![CDATA[ 13 <![CDATA[
15 #from datetime import datetime 14 #from datetime import datetime
16 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") 15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
17 #set $samp_str = "Sample_%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")
18 #set $temp_stderr = "searchgui_stderr" 17 #set $temp_stderr = "searchgui_stderr"
18 #set $bin_dir = "bin"
19 19
20 mkdir output; 20 mkdir output;
21 mkdir output_reports; 21 mkdir output_reports;
22 cwd=`pwd`; 22 cwd=`pwd`;
23 export HOME=\$cwd; 23 export HOME=\$cwd;
24 24
25 ## echo the search engines to run
26 echo "$engines";
27 echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}";
28
25 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present 29 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
26 echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties; 30 echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties;
27
28 cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin;
29 tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`;
30 31
31 #for $mgf in $peak_lists: 32 #for $mgf in $peak_lists:
32 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" 33 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
33 ln -s -f '${mgf}' '${input_name}'; 34 ln -s -f '${mgf}' '${input_name}';
35 #set $encoded_id = $__app__.security.encode_id($mgf.id)
36 echo "Spectrums:${mgf.display_name}(API:${encoded_id}) ";
34 #end for 37 #end for
35 ##ln -s "${input_database}" input_database.fasta; 38 ##ln -s "${input_database}" input_database.fasta;
36 cp "${input_database}" input_database.fasta; 39 cp "${input_database}" input_database.fasta;
37 40
38 ########################################### 41 ###########################################
39 #### Creating decoy database #### 42 #### Creating decoy database ####
40 ########################################### 43 ###########################################
41 #if $create_decoy: 44 #if $create_decoy:
42 echo "Creating decoy database."; 45 echo "Creating decoy database.";
43 java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy && 46 searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy &&
44 rm input_database.fasta && 47 rm input_database.fasta &&
45 cp input_database_concatenated_target_decoy.fasta input_database.fasta && 48 cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
46 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; 49 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
47 #end if 50 #end if
48 51
49 ##################################################### 52 #####################################################
50 ## generate IdentificationParameters for SearchGUI ## 53 ## generate IdentificationParameters for SearchGUI ##
51 ##################################################### 54 #####################################################
52 55 (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
53 (java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI 56 --exec_dir="\$cwd/${bin_dir}"
54 -out SEARCHGUI_IdentificationParameters.par 57 -out SEARCHGUI_IdentificationParameters.par
55 58
56 @GENERAL_PARAMETERS@ 59 @GENERAL_PARAMETERS@
57 60
58 -db input_database.fasta 61 -db input_database.fasta
59 $use_gene_mapping 62 #if $use_gene_mapping:
63 $use_gene_mapping
64 $update_gene_mapping
65 #end if
60 66
61 #if $xtandem.xtandem_advanced == "yes" 67 #if $xtandem.xtandem_advanced == "yes"
62 68
63 -xtandem_npeaks ${xtandem.xtandem_npeaks} 69 -xtandem_npeaks ${xtandem.xtandem_npeaks}
64 -xtandem_min_peaks ${xtandem.xtandem_min_peaks} 70 -xtandem_min_peaks ${xtandem.xtandem_min_peaks}
194 -andromeda_frag_method ${andromeda.andromeda_frag_method} 200 -andromeda_frag_method ${andromeda.andromeda_frag_method}
195 -andromeda_max_mods ${andromeda.andromeda_max_mods} 201 -andromeda_max_mods ${andromeda.andromeda_max_mods}
196 -andromeda_min_pep_length ${andromeda.andromeda_min_pep_length} 202 -andromeda_min_pep_length ${andromeda.andromeda_min_pep_length}
197 -andromeda_max_pep_length ${andromeda.andromeda_max_pep_length} 203 -andromeda_max_pep_length ${andromeda.andromeda_max_pep_length}
198 -andromeda_max_psms ${andromeda.andromeda_max_psms} 204 -andromeda_max_psms ${andromeda.andromeda_max_psms}
205 -andromeda_decoy_mode ${andromeda.andromeda_decoy_mode}
199 #end if 206 #end if
200 *# 207 *#
201 208
202 #* Not working in tests 209 #* Not working in tests
203 #if $tide.tide_advanced == "yes" 210 #if $tide.tide_advanced == "yes"
243 #if $comet.comet_advanced == "yes" 250 #if $comet.comet_advanced == "yes"
244 251
245 #if $comet.comet_spectrum.comet_spectrum_selector == "yes" 252 #if $comet.comet_spectrum.comet_spectrum_selector == "yes"
246 -comet_min_peaks ${comet.comet_spectrum.comet_min_peaks} 253 -comet_min_peaks ${comet.comet_spectrum.comet_min_peaks}
247 -comet_min_peak_int ${comet.comet_spectrum.comet_min_peak_int} 254 -comet_min_peak_int ${comet.comet_spectrum.comet_min_peak_int}
248 -comet_remove_prec ${comet.comet_spectrum.comet_remove_prec} 255
249 256 -comet_remove_prec ${comet.comet_spectrum.comet_prec.comet_remove_prec}
250 257
251 #if $comet.comet_spectrum.comet_remove_prec == "1" 258
252 -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol} 259 #if $comet.comet_spectrum.comet_prec.comet_remove_prec == "1"
260 -comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
253 #end if 261 #end if
254 262
255 #if $comet.comet_spectrum.comet_remove_prec == "2" 263 #if $comet.comet_spectrum.comet_prec.comet_remove_prec == "2"
256 -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol} 264 -comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
257 #end if 265 #end if
258 266
259 -comet_clear_mz_range_lower ${comet.comet_spectrum.comet_clear_mz_range_lower} 267 -comet_clear_mz_range_lower ${comet.comet_spectrum.comet_clear_mz_range_lower}
260 -comet_clear_mz_range_upper ${comet.comet_spectrum.comet_clear_mz_range_upper} 268 -comet_clear_mz_range_upper ${comet.comet_spectrum.comet_clear_mz_range_upper}
261 #end if 269 #end if
277 -comet_sparse_matrix ${comet.comet_fragment_ions.comet_sparse_matrix} 285 -comet_sparse_matrix ${comet.comet_fragment_ions.comet_sparse_matrix}
278 -comet_theoretical_fragment_ions ${comet.comet_fragment_ions.comet_theoretical_fragment_ions} 286 -comet_theoretical_fragment_ions ${comet.comet_fragment_ions.comet_theoretical_fragment_ions}
279 #end if 287 #end if
280 #end if 288 #end if
281 289
290 #if $directtag.directtag_advanced == "yes"
291 -directag_tic_cutoff ${directtag.directag_tic_cutoff}
292 -directag_max_peak_count ${directtag.directag_max_peak_count}
293 -directag_intensity_classes ${directtag.directag_intensity_classes}
294 -directag_adjust_precursor ${directtag.directag_adjust_precursor}
295 -directag_min_adjustment ${directtag.directag_min_adjustment}
296 -directag_max_adjustment ${directtag.directag_max_adjustment}
297 -directag_adjustment_step ${directtag.directag_adjustment_step}
298 -directag_charge_states ${directtag.directag_charge_states}
299 #if str($directtag.directag_output_suffix).strip() != '':
300 -directag_output_suffix ${directtag.directag_output_suffix}
301 #end if
302 -directag_ms_charge_state ${directtag.directag_ms_charge_state}
303 -directag_duplicate_spectra ${directtag.directag_duplicate_spectra}
304 -directag_deisotoping ${directtag.directag_deisotoping}
305 -directag_isotope_tolerance ${directtag.directag_isotope_tolerance}
306 -directag_complement_tolerance ${directtag.directag_complement_tolerance}
307 -directag_tag_length ${directtag.directag_tag_length}
308 -directag_max_var_mods ${directtag.directag_max_var_mods}
309 -directag_max_tag_count ${directtag.directag_max_tag_count}
310 -directag_intensity_weight ${directtag.directag_intensity_weight}
311 -directag_fidelity_weight ${directtag.directag_fidelity_weight}
312 -directag_complement_weight ${directtag.directag_complement_weight}
313 #end if
314
315 #if $novor.novor_advanced == "yes"
316 -novor_fragmentation ${novor.novor_fragmentation}
317 -novor_mass_analyzer ${novor.novor_mass_analyzer}
318 #end if
319
282 2> $temp_stderr) 320 2> $temp_stderr)
283 && 321 &&
284 322
285 ################ 323 ################
286 ## Search CLI ## 324 ## Search CLI ##
287 ################ 325 ################
288 (java -Djava.awt.headless=true -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.SearchCLI 326 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
327 --exec_dir="\$cwd/${bin_dir}"
289 -temp_folder `pwd` 328 -temp_folder `pwd`
290 -spectrum_files \$cwd 329 -spectrum_files \$cwd
291 -output_folder \$cwd/output 330 -output_folder \$cwd/output
292 -id_params SEARCHGUI_IdentificationParameters.par 331 -id_params SEARCHGUI_IdentificationParameters.par
293 332
351 390
352 #if 'Andromeda' in $engines_list: 391 #if 'Andromeda' in $engines_list:
353 -andromeda 1 392 -andromeda 1
354 #else 393 #else
355 -andromeda 0 394 -andromeda 0
395 #end if
396
397 #if 'Novor' in $engines_list:
398 -novor 1
399 #else
400 -novor 0
401 #end if
402
403 #if 'DirecTag' in $engines_list:
404 -directag 1
405 #else
406 -directag 0
356 #end if 407 #end if
357 408
358 ## single zip file 409 ## single zip file
359 -output_option 0 410 -output_option 0
360 411
386 help="Selecting this option will help PeptideShaker calculate FDR values" /> 437 help="Selecting this option will help PeptideShaker calculate FDR values" />
387 438
388 <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false" 439 <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false"
389 label="gene mappings will be used and saved along with the project (UniProt databases only)" 440 label="gene mappings will be used and saved along with the project (UniProt databases only)"
390 help="This should only be enabled for UniProt databaases" /> 441 help="This should only be enabled for UniProt databaases" />
442 <param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false"
443 label="Update gene mappings automatically from Ensembl (UniProt databases only)"
444 help="This should only be enabled for UniProt databaases" />
391 445
392 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)" 446 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
393 help="Select appropriate MGF dataset(s) from history" /> 447 help="Select appropriate MGF dataset(s) from history" />
394 448
395 <!-- Search Engine Selection --> 449 <!-- Search Engine Selection -->
396 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> 450 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
397 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help> 451 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
398 <option value="X!Tandem" selected="True">X!Tandem</option> 452 <option value="X!Tandem" selected="True">X!Tandem</option>
399 <!-- Not working in tests 453
400 <option value="MyriMatch">MyriMatch</option>
401 <option value="MS_Amanda">MS_Amanda</option>
402 -->
403 <option value="MSGF" selected="True">MS-GF+</option> 454 <option value="MSGF" selected="True">MS-GF+</option>
404 <option value="OMSSA" selected="True">OMSSA</option> 455 <option value="OMSSA" selected="True">OMSSA</option>
405 <option value="Comet">Comet</option> 456 <option value="Comet">Comet</option>
406 <!-- Not working in tests 457 <!-- Not working in tests
458 -->
407 <option value="Tide">Tide</option> 459 <option value="Tide">Tide</option>
460 <!-- Not working in tests
408 --> 461 -->
462 <option value="MyriMatch">MyriMatch</option>
463 <option value="MS_Amanda">MS_Amanda</option>
409 <!-- Windows only 464 <!-- Windows only
410 <option value="Andromeda">Andromeda</option> 465 <option value="Andromeda">Andromeda</option>
411 --> 466 -->
467 <!-- New with version 3.0
468 -->
469 <!--working in tests
470 -->
471 <option value="DirecTag">DirecTag</option>
472 <option value="Novor">Novor (Select for non-commercial use only)</option>
412 <validator type="no_options" message="Please select at least one output file" /> 473 <validator type="no_options" message="Please select at least one output file" />
413 </param> 474 </param>
414 475
415 476
416 <!-- General Parameters --> 477 <!-- General Parameters -->
437 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf" 498 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
438 help="Choose a smaller value if you are running on a machine with limited memory"/> 499 help="Choose a smaller value if you are running on a machine with limited memory"/>
439 500
440 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" 501 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
441 help="Choose a smaller value if you are running on a machine with limited memory"/> 502 help="Choose a smaller value if you are running on a machine with limited memory"/>
442 </when> 503 </when>
443 </conditional> 504 </conditional>
444 505
445 506
446 <!-- X!TANDEM ADVANCED PARAMETERS --> 507 <!-- X!TANDEM ADVANCED PARAMETERS -->
447 <conditional name="xtandem"> 508 <conditional name="xtandem">
468 <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection" 529 <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
469 label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" /> 530 label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" />
470 <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models" 531 <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
471 label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" /> 532 label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" />
472 <param name="xtandem_evalue" help="Highest value for recorded peptides" 533 <param name="xtandem_evalue" help="Highest value for recorded peptides"
473 label="X!Tandem: Maximum Valid Expectation Value" type="float" value="100" /> 534 label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" />
474 <param name="xtandem_output_proteins" help="Controls output of protein sequences" 535 <param name="xtandem_output_proteins" help="Controls output of protein sequences"
475 label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" /> 536 label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
476 <param name="xtandem_output_sequences" help="Controls output of sequence information" 537 <param name="xtandem_output_sequences" help="Controls output of sequence information"
477 label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" /> 538 label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
478 <param name="xtandem_output_spectra" help="Controls output of spectrum information" 539 <param name="xtandem_output_spectra" help="Controls output of spectrum information"
865 </param> 926 </param>
866 <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" /> 927 <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" />
867 <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" /> 928 <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" />
868 <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" /> 929 <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" />
869 <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" /> 930 <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" />
931 <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" />
870 </when> 932 </when>
871 </conditional> 933 </conditional>
872 --> 934 -->
873 935
874 <!-- Comet ADVANCED PARAMETERS --> 936 <!-- Comet ADVANCED PARAMETERS -->
889 <when value="yes"> 951 <when value="yes">
890 <param name="comet_min_peaks" type="integer" value="10" 952 <param name="comet_min_peaks" type="integer" value="10"
891 label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" /> 953 label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" />
892 <param name="comet_min_peak_int" type="float" value="0.0" 954 <param name="comet_min_peak_int" type="float" value="0.0"
893 label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" /> 955 label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" />
894 <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal"> 956 <conditional name="comet_prec">
895 <option value="0" selected="True" >off</option> 957 <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal">
896 <option value="1">on</option> 958 <option value="0" selected="True" >off</option>
897 <option value="2">as expected for ETD/ECD spectra</option> 959 <option value="1">on</option>
898 </param> 960 <option value="2">as expected for ETD/ECD spectra</option>
899 <when value="0" /> 961 </param>
900 <when value="1"> 962 <when value="0" />
901 <param name="comet_remove_prec_tol" type="float" value="1.5" 963 <when value="1">
902 label="Comet: Remove Precursor Tolerance" /> 964 <param name="comet_remove_prec_tol" type="float" value="1.5"
903 </when> 965 label="Comet: Remove Precursor Tolerance" />
904 <when value="2"> 966 </when>
905 <param name="comet_remove_prec_tol" type="float" value="1.5" 967 <when value="2">
906 label="Comet: Remove Precursor Tolerance" /> 968 <param name="comet_remove_prec_tol" type="float" value="1.5"
907 </when> 969 label="Comet: Remove Precursor Tolerance" />
970 </when>
971 </conditional>
908 <param name="comet_clear_mz_range_lower" type="float" value="0.0" 972 <param name="comet_clear_mz_range_lower" type="float" value="0.0"
909 label="Comet: Minimum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, lower m/z range" /> 973 label="Comet: Minimum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, lower m/z range" />
910 <param name="comet_clear_mz_range_upper" type="float" value="0.0" 974 <param name="comet_clear_mz_range_upper" type="float" value="0.0"
911 label="Comet: Maximum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, upper m/z range" /> 975 label="Comet: Maximum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, upper m/z range" />
912 </when> 976 </when>
962 label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" /> 1026 label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" />
963 </when> 1027 </when>
964 </conditional> 1028 </conditional>
965 </when> 1029 </when>
966 </conditional> 1030 </conditional>
1031 <conditional name="directtag">
1032 <param name="directtag_advanced" type="select" label="DirectTag Options">
1033 <option value="yes">Advanced</option>
1034 <option value="no" selected="True">Default</option>
1035 </param>
1036 <when value="no" />
1037 <when value="yes">
1038 <param name="directag_tic_cutoff" type="integer" value="85" label="DirecTag TIC cutoff in percent, default is '85'."/>
1039 <param name="directag_max_peak_count" type="integer" value="400" label="DirecTag max peak count, default is '400'."/>
1040 <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses, default is '3'."/>
1041 <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor, default is false."/>
1042 <param name="directag_min_adjustment" type="float" value="-2.5" label="DirecTag minimum precursor adjustment, default is '-2.5'."/>
1043 <param name="directag_max_adjustment" type="float" value="2.5" label="DirecTag maximum precursor adjustment, default is '2.5'."/>
1044 <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step, default is '0.1'."/>
1045 <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered, default is '3'."/>
1046 <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix, default is no suffix."/>
1047 <param name="directag_ms_charge_state" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag use charge state from M spectrum, default is false."/>
1048 <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/>
1049 <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping">
1050 <option value="0" selected="true">no deisotoping</option>
1051 <option value="1">precursor only</option>
1052 <option value="2">precursor and candidate</option>
1053 </param>
1054 <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is '0.25'."/>
1055 <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is '0.5'."/>
1056 <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is '3'."/>
1057 <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is '2'."/>
1058 <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is '20'."/>
1059 <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is '1.0'."/>
1060 <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is '1.0'."/>
1061 <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight, default is '1.0'."/>
1062 </when>
1063 </conditional>
1064
1065 <conditional name="novor">
1066 <param name="novor_advanced" type="select" label="Novor Options">
1067 <option value="yes">Advanced</option>
1068 <option value="no" selected="True">Default</option>
1069 </param>
1070 <when value="no" />
1071 <when value="yes">
1072 <param name="novor_fragmentation" type="select" label="Novor fragmentation method">
1073 <option value="HCD" selected="True">HCD</option>
1074 <option value="CID">CID</option>
1075 </param>
1076 <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra">
1077 <option value="FT" selected="True">FT</option>
1078 <option value="Trap" >Trap</option>
1079 <option value="TOF" >TOF</option>
1080 </param>
1081 </when>
1082 </conditional>
1083
967 </inputs> 1084 </inputs>
968 <outputs> 1085 <outputs>
969 <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> 1086 <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
970 </outputs> 1087 </outputs>
971 <tests> 1088 <tests>
981 <param name="max_charge" value="3"/> 1098 <param name="max_charge" value="3"/>
982 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> 1099 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
983 <param name="xtandem.xtandem_advanced" value="yes"/> 1100 <param name="xtandem.xtandem_advanced" value="yes"/>
984 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/> 1101 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
985 1102
986 <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="600" /> 1103 <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
987 </test> 1104 </test>
988
989 <!-- Test that search works with MSAmanda --> 1105 <!-- Test that search works with MSAmanda -->
990 <test> 1106 <test>
991 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> 1107 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
992 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> 1108 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
993 <param name="precursor_ion_tol" value="100"/> 1109 <param name="precursor_ion_tol" value="100"/>
995 <param name="variable_modifications" value="oxidation of m"/> 1111 <param name="variable_modifications" value="oxidation of m"/>
996 <param name="min_charge" value="1"/> 1112 <param name="min_charge" value="1"/>
997 <param name="max_charge" value="3"/> 1113 <param name="max_charge" value="3"/>
998 <param name="engines" value="MS_Amanda"/> 1114 <param name="engines" value="MS_Amanda"/>
999 1115
1000 <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="600" /> 1116 <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
1001 </test> 1117 </test>
1002
1003
1004 </tests> 1118 </tests>
1005 <help> 1119 <help>
1006 **What it does** 1120 **What it does**
1007 1121
1008 Runs multiple search engines on any number of MGF peak lists using the SearchGUI. 1122 Runs multiple search engines on any number of MGF peak lists using the SearchGUI.