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comparison peptide_shaker.xml @ 14:db6cc184146c draft

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author galaxyp
date Fri, 19 Jul 2013 11:39:19 -0400
parents 6521f577059f
children d90e25c7b492
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13:6521f577059f 14:db6cc184146c
224 For the underlying tool, please cite `TODO` 224 For the underlying tool, please cite `TODO`
225 225
226 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker 226 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker
227 </help> 227 </help>
228 </tool> 228 </tool>
229 <tool id="peptide_shaker" name="Peptide Shaker" version="0.1.0">
230 <!-- TODO: Set defaults for weights correctly -->
231 <description>
232 Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline.
233 </description>
234 <command>
235 #from datetime import datetime
236 #set $exp_str = "Galaxy Experiment %s" % datetime.now().strftime("%Y%m%d%H%M%s")
237 #set $samp_str = "Sample %s" % datetime.now().strftime("%Y%m%d%H%M%s")
238 mkdir spectra;
239 mkdir output;
240 mkdir output_reports;
241 cwd=`pwd`;
242 #for $mgf in $peak_lists:
243 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
244 ln -s '$mgf' 'spectra/$input_name';
245 #end for
246 SearchCLI \
247 -spectrum_files \$cwd/spectra \
248 -output_folder \$cwd/output \
249 -ppm $precursor_ion_tol_units \
250 -prec_tol $precursor_ion_tol \
251 -frag_tol $fragment_tol \
252 -enzyme '$enzyme' \
253 #set $fixed_mods_str = $fixed_modifications or ''
254 #set $variable_mods_str = $variable_modifications or ''
255 #if $fixed_mods_str
256 -fixed_mods "$fixed_mods_str" \
257 #end if
258 #if $variable_mods_str
259 -variable_mods "$variable_mods_str" \
260 #end if
261 -mc $missed_cleavages \
262 #if $advanced.specify:
263 -xtandem $advanced.xtandem \
264 #if $advanced.omssa.run_omssa
265 #set $omssa = 1
266 #else
267 #set $omssa = 0
268 #end if
269 -omssa $omssa \
270 #if $omssa == 1
271 -hitlist_length ${advanced.omssa.hitlist_length} \
272 -remove_prec ${advanced.omssa.remove_precursor} \
273 -scale_prec ${advanced.omssa.scale_precursor} \
274 -estimate_charge ${advanced.omssa.estimate_charge} \
275 #end if
276 #end if
277 -db $input_database;
278 PeptideShakerCLI \
279 -experiment '$exp_str' \
280 -sample '$samp_str' \
281 -replicate 1 \
282 -spectrum_files \$cwd/spectra \
283 -identification_files \$cwd/output \
284 -search_params \$cwd/output/SearchGUI.parameters \
285 -out_txt_1 \$cwd/output_reports \
286 #if $processing_options.specify
287 -protein_FDR ${processing_options.protein_fdr} \
288 -peptide_FDR ${processing_options.peptide_fdr} \
289 -psm_FDR ${processing_options.psm_fdr} \
290 -psm_FLR ${processing_options.psm_flr} \
291 #if str($processing_options.a_score.use) == "1"
292 #set $a_score = 1
293 #else
294 #set $a_score = 0
295 #end if
296 -a_score $a_score \
297 #if str($a_score) == "1"
298 -a_score_neutral_losses ${processing_options.a_score.neutral_losses} \
299 #end if
300 #end if
301 #if $filtering_options.specify
302 -min_peptide_length ${filtering_options.min_peptide_length} \
303 -max_peptide_length ${filtering_options.max_peptide_length} \
304 -max_precursor_error ${filtering_options.max_precursor_error} \
305 -max_precursor_error_type ${filtering_options.max_precursor_error_type} \
306 -max_xtandem_e ${filtering_options.max_xtandem_e} \
307 -max_omssa_e ${filtering_options.max_omssa_e} \
308 -exclude_unknown_ptms ${filtering_options.exclude_unknown_ptms} \
309 #end if
310 -out \$cwd/output.cps ;
311 mv output_reports/*peptides.txt peptides.txt ;
312 mv output_reports/*psms.txt psms.txt ;
313 mv output_reports/*proteins.txt proteins.txt
314 </command>
315 <stdio>
316 <exit_code range="1:" level="fatal" description="Job Failed" />
317 </stdio>
318 <inputs>
319 <param format="fasta" name="input_database" type="data" label="Protein Database"/>
320 <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" />
321 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units">
322 <option value="1">Parts per million (ppm)</option>
323 <option value="0">Daltons</option>
324 </param>
325 <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" />
326 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" />
327 <param name="enzyme" type="select" label="Enzyme">
328 <option value="Trypsin">Trypsin</option>
329 <option value="Arg-C">Arg-C</option>
330 <option value="CNBr">CNBr</option>
331 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
332 <option value="Formic Acid">Formic Acid</option>
333 <option value="Lys-C">Lys-C</option>
334 <option value="Lys-C, no P rule">Lys-C, no P rule</option>
335 <option value="Pepsin A">Pepsin A</option>
336 <option value="Trypsin + CNBr">Trypsin + CNBr</option>
337 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
338 <option value="Trypsin, no P rule">Trypsin, no P rule</option>
339 <option value="whole protein">whole protein</option>
340 <option value="Asp-N">Asp-N</option>
341 <option value="Glu-C">Glu-C</option>
342 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
343 <option value="Top-Down">Top-Down</option>
344 <option value="Semi-Tryptic">Semi-Tryptic</option>
345 <option value="No enzyme">No enzyme</option>
346 <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
347 <option value="Asp-N (DE)">Asp-N (DE)</option>
348 <option value="Glu-C (DE)">Glu-C (DE)</option>
349 <option value="Lys-N (K)">Lys-N (K)</option>
350 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
351 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
352 <option value="Semi-Glu-C">Semi-Glu-C</option>
353 </param>
354 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" />
355 <param name="fixed_modifications" type="select" label="Fixed Modification" multiple="true">
356 <options from_file="searchgui_mods.loc">
357 <column name="name" index="0" />
358 <column name="value" index="0" />
359 </options>
360 </param>
361 <param name="variable_modifications" type="select" label="Variable Modification" multiple="true">
362 <options from_file="searchgui_mods.loc">
363 <column name="name" index="0" />
364 <column name="value" index="0" />
365 </options>
366 </param>
367 <param name="min_charge" label="Minimum Charge" value="2" type="integer" />
368 <param name="max_charge" label="Maximum Charge" value="4" type="integer" />
369 <param name="forward_ion" label="Forward Ion" type="select">
370 <option value="a">a</option>
371 <option value="b" selected="true">b</option>
372 <option value="c">c</option>
373 </param>
374 <param name="reverse_ion" label="Reverse Ion" type="select">
375 <option value="x">x</option>
376 <option value="y" selected="true">y</option>
377 <option value="z">z</option>
378 </param>
379 <conditional name="advanced">
380 <param name="specify" label="Specify Advanced Search Options" type="boolean" truevalue="true" falsevalue="false" />
381 <when value="false" />
382 <when value="true">
383 <param name="xtandem" label="Run X! Tandem" type="boolean" truevalue="1" falsevalue="0" checked="true" />
384 <conditional name="omssa">
385 <param name="run_omssa" label="Run OMSSA" type="boolean" truevalue="1" falsevalue="0" checked="true" />
386 <when value="0" />
387 <when value="1">
388 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
389 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
390 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
391 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
392 </when>
393 </conditional>
394 </when>
395 </conditional>
396 <conditional name="processing_options">
397 <param name="specify" label="Specify Advanced PeptideShaker Processing Options" type="boolean" truevalue="true" falsevalue="false" />
398 <when value="false" />
399 <when value="true">
400 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
401 <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
402 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
403 <param name="psm_flr" label="FLR at the PSM level" help="In percent (default 1% FLR: '1'). Percent for peptides with different potential modification sites and one variable modification." value="1" type="float" />
404 <conditional name="a_score">
405 <param name="use" label="Calculate A Score" type="boolean" truevalue="1" falsevalue="0" checked="true" />
406 <when value="0" />
407 <when value="1">
408 <param name="neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
409 </when>
410 </conditional>
411 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
412 </when>
413 </conditional>
414 <conditional name="filtering_options">
415 <param name="specify" label="Specify Advanced PeptideShaker Filtering Options" type="boolean" truevalue="true" falsevalue="false" />
416 <when value="false" />
417 <when value="true">
418 <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" />
419 <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" />
420 <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." />
421 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
422 <option value="0">ppm</option>
423 <option value="1">Daltons</option>
424 </param>
425 <param name="max_xtandem_e" label="Maximum X! Tandem E Value" value="100" type="float" help="" />
426 <param name="max_omssa_e" label="Maximum OMSSA E Value" value="100" type="float" help="" />
427 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
428 </when>
429 </conditional>
430 </inputs>
431 <outputs>
432 <data format="cps" name="output" label="PeptideShaker CPS results for ${on_string}" from_work_dir="output.cps" />
433 <data format="tabular" name="output_peptides" label="PeptideShaker Peptide Report for ${on_string}" from_work_dir="peptides.txt" />
434 <data format="tabular" name="output_proteins" label="PeptideShaker Protein Report for ${on_string}" from_work_dir="proteins.txt" />
435 <data format="tabular" name="output_psms" label="PeptideShaker PSM Report for ${on_string}" from_work_dir="psms.txt" />
436 </outputs>
437 <requirements>
438 <requirement type="package" version="0.20.1">PeptideShaker</requirement>
439 <requirement type="package" version="1.14.1">SearchGUI</requirement>
440 </requirements>
441 <help>
442 **What it does**
443
444 Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the result via PeptideShaker.
445
446 ------
447
448 **Citation**
449
450 For the underlying tool, please cite `TODO`
451
452 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker
453 </help>
454 </tool>