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comparison pepquery2.xml @ 2:3b2874c58bcd draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
author galaxyp
date Tue, 25 Oct 2022 16:06:20 +0000
parents 6b5ce9e2b0d0
children d8962e547c9c
comparison
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1:6b5ce9e2b0d0 2:3b2874c58bcd
30 #raise ValueError 30 #raise ValueError
31 #end if 31 #end if
32 #end if 32 #end if
33 ## PepQuery command 33 ## PepQuery command
34 pepquery 34 pepquery
35 -Xmx\$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]g
35 #if $validation.task_type == "known" 36 #if $validation.task_type == "known"
36 -s 2 $validation.decoy 37 -s 2 $validation.decoy
37 #else 38 #else
38 -s 1 39 -s 1
39 #end if 40 #end if
47 -db '$db_file' 48 -db '$db_file'
48 #else 49 #else
49 -db '$req_inputs.db_type.db_id' 50 -db '$req_inputs.db_type.db_id'
50 #end if 51 #end if
51 #if $req_inputs.input_type.input_type_selector == 'peptide' 52 #if $req_inputs.input_type.input_type_selector == 'peptide'
52 -t '$req_inputs.input_type.input_type_selector' 53 -t $req_inputs.input_type.input_type_selector
53 -i '$req_inputs.input_type.multiple.input' 54 -i '$req_inputs.input_type.multiple.input'
54 #else 55 #else
55 -t '$req_inputs.input_type.input_type_selector' 56 -t $req_inputs.input_type.input_type_selector
56 #if int(str($req_inputs.input_type.input_type_selector)) == 1 57 #if $req_inputs.input_type.input_type_selector == 'protein'
57 -i '$req_inputs.input_type.multiple.input' 58 #if $req_inputs.input_type.multiple.protein_input_selector == 'identifier'
59 #set $prot_id = str($req_inputs.input_type.multiple.input).replace('|','\|')
60 -i '"$prot_id"'
61 #else
62 -i '$req_inputs.input_type.multiple.input'
63 #end if
58 #else 64 #else
59 -i '$req_inputs.input_type.input' 65 -i '$req_inputs.input_type.input'
60 #if int(str($req_inputs.input_type.input_type_selector)) == 2 66 #if $req_inputs.input_type.input_type_selector == 'DNA'
61 #if $req_inputs.input_type.frame == 'None' 67 #if $req_inputs.input_type.frame == 'None'
62 -f '0' 68 -frame '0'
63 #else 69 #else
64 -f '$req_inputs.input_type.frame' 70 -frame '$req_inputs.input_type.frame'
65 #end if 71 #end if
66 #else 72 #else
67 -anno '$req_inputs.input_type.anno' 73 -anno '$req_inputs.input_type.anno'
68 #end if 74 #end if
69 #end if 75 #end if
70 #end if 76 #end if
77 #if $req_inputs.indexType
71 -indexType $req_inputs.indexType 78 -indexType $req_inputs.indexType
79 #end if
72 80
73 #if $modifications.fixed_mod 81 #if $modifications.fixed_mod
74 -fixMod '$modifications.fixed_mod' 82 -fixMod '$modifications.fixed_mod'
75 #end if 83 #end if
76 #if $modifications.var_mod 84 #if $modifications.var_mod
132 #if 'psm_annotation.txt' in $outputs_selected 140 #if 'psm_annotation.txt' in $outputs_selected
133 -plot 141 -plot
134 #end if 142 #end if
135 $fast 143 $fast
136 -o pepquery_output 144 -o pepquery_output
137 | sed 's/No valid peptide/Error: No valid peptide/' | tee >(cat 1>&2) 145 | tee >(sed "s/\x1b[^m]*m//g" > log.txt)
138 #set $flist = str($outputs_selected).replace(',',' ') 146 #set $flist = str($outputs_selected).replace(',',' ').replace('ms_index','')
139 && for i in $flist; do for f in `find pepquery_output/*/* -name \$i`; do cat \$f >> pepquery_output/\${i}; done; done 147 && for i in $flist; do for f in `find pepquery_output/*/* -name \$i`; do cat \$f >> pepquery_output/\${i}; done; done
140 && for f in `find pepquery_output/*/ -name parameter.txt`; do cp \$f pepquery_output/parameter.txt; done 148 && for f in `find pepquery_output/*/ -name parameter.txt`; do cp \$f pepquery_output/parameter.txt; done
141 ]]> 149 ]]>
142 </command> 150 </command>
143 <inputs> 151 <inputs>
153 </conditional> 161 </conditional>
154 <section name="req_inputs" title="Input Data" expanded="true"> 162 <section name="req_inputs" title="Input Data" expanded="true">
155 <conditional name="input_type"> 163 <conditional name="input_type">
156 <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" > 164 <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" >
157 <option value="peptide">peptide</option> 165 <option value="peptide">peptide</option>
158 <option value="1">protein</option> 166 <option value="protein">protein</option>
159 <option value="2">DNA (translate to protein sequences)</option> 167 <option value="DNA">DNA (translate to protein sequences)</option>
160 <!-- these are not working with pepquery version 1.6 168 <!-- these are not working with pepquery version 1.6
161 <option value="3">VCF (translate to protein sequences)</option> 169 <option value="3">VCF (translate to protein sequences)</option>
162 <option value="4">BED (translate to protein sequences)</option> 170 <option value="4">BED (translate to protein sequences)</option>
163 <option value="5">GTF (translate to protein sequences)</option> 171 <option value="5">GTF (translate to protein sequences)</option>
164 --> 172 -->
168 <param name="peptide_input_selector" type="select" label="Peptides?"> 176 <param name="peptide_input_selector" type="select" label="Peptides?">
169 <option value="multiple">Peptide list from your history</option> 177 <option value="multiple">Peptide list from your history</option>
170 <option value="single">Single peptide entered as text</option> 178 <option value="single">Single peptide entered as text</option>
171 </param> 179 </param>
172 <when value="multiple"> 180 <when value="multiple">
173 <param name="input" argument="-i" type="data" format="txt" label="Peptide Sequences (.txt)" help="Peptide sequence file containing peptides which you want to search (no column header, 1 peptide per line)." /> 181 <param name="input" argument="-i" type="data" format="txt" label="Peptide Sequences (.txt)">
182 <help>Peptide sequence file containing peptides which you want to search (no column headers).
183 First column is am peptide sequence. Optional second column is spectrum title.
184 </help>
185 </param>
174 </when> 186 </when>
175 <when value="single"> 187 <when value="single">
176 <param name="input" argument="-i" type="text" label="Peptide Sequence" help="Peptide sequence(s) which you want to search"> 188 <param name="input" argument="-i" type="text" label="Peptide Sequence" help="Peptide sequence(s) which you want to search">
177 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+(,[AC-IK-NP-TV-Yac-ik-np-tv-y]+)*$</validator> 189 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+(,[AC-IK-NP-TV-Yac-ik-np-tv-y]+)*$</validator>
178 </param> 190 </param>
179 </when> 191 </when>
180 </conditional> 192 </conditional>
181 </when> 193 </when>
182 <when value="1"> 194 <when value="protein">
183 <conditional name="multiple"> 195 <conditional name="multiple">
184 <param name="protein_input_selector" type="select" label="Proteins?"> 196 <param name="protein_input_selector" type="select" label="Proteins?">
185 <option value="multiple">Protein fasta from your history</option> 197 <option value="multiple">Protein fasta from your history</option>
186 <option value="single">Single protein entered as text</option> 198 <option value="single">Single protein entered as text</option>
199 <option value="identifier">Protein Identifier from selected Protein Reference Database</option>
187 </param> 200 </param>
188 <when value="multiple"> 201 <when value="multiple">
189 <param name="input" argument="-i" type="data" format="fasta" label="Protein Sequences (.txt)" help="Protein fasta file containing proteins which you want to search." /> 202 <param name="input" argument="-i" type="data" format="fasta" label="Protein Sequences (.txt)" help="Protein fasta file containing proteins which you want to search." />
190 </when> 203 </when>
191 <when value="single"> 204 <when value="single">
192 <param name="input" argument="-i" type="text" label="Protein Sequence" help="Protein sequence which you want to search"> 205 <param name="input" argument="-i" type="text" label="Protein Sequence" help="Protein sequence which you want to search">
193 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator> 206 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator>
194 </param> 207 </param>
195 </when> 208 </when>
209 <when value="identifier">
210 <param name="input" argument="-i" type="text" label="Protein Identifier" help="Protein ID from the selected Protein Reference Database. E.g. sp|P07205|PGK2_HUMAN from swissprot:human">
211 <sanitizer invalid_char="">
212 <valid initial="string.ascii_letters,string.digits">
213 <add value="|" />
214 </valid>
215 </sanitizer>
216 <validator type="regex" message="Spaces not allowed in ID">^[^ ]+$</validator>
217 </param>
218 </when>
196 </conditional> 219 </conditional>
197 </when> 220 </when>
198 <when value="2"> 221 <when value="DNA">
199 <param name="input" argument="-i" type="text" label="DNA Sequence (at least 60 bp)" help="DNA sequence which you want to search"> 222 <param name="input" argument="-i" type="text" label="DNA Sequence (at least 60 bp)" help="DNA sequence which you want to search">
200 <validator type="regex" message="Must be at least 60bp">^[acgtuAGCTU]{60}[acgtuAGCTU]*$</validator> 223 <validator type="regex" message="Must be at least 60bp">^[acgtuAGCTU]{60}[acgtuAGCTU]*$</validator>
201 </param> 224 </param>
202 <param name="frame" argument="-f" type="select" label="Frame(s) for DNA translation" multiple="true" help="The frame(s) to translate DNA sequence to protein. Selecting nothing (default) keeps the longest frame"> 225 <param name="frame" argument="-f" type="select" label="Frame(s) for DNA translation" multiple="true" help="The frame(s) to translate DNA sequence to protein. Selecting nothing (default) keeps the longest frame">
203 <option value="1">1</option> 226 <option value="1">1</option>
266 <validator type="regex" message="An identifier strating with PXD or MSV or JPST">^(PXD|MSV|JPST).*$</validator> 289 <validator type="regex" message="An identifier strating with PXD or MSV or JPST">^(PXD|MSV|JPST).*$</validator>
267 </param> 290 </param>
268 </when> 291 </when>
269 </conditional> 292 </conditional>
270 293
271 <param name="indexType" argument="-indexType" type="select" label="Report Spectrum Scan as" help="" > 294 <param name="indexType" argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" >
272 <option value="1" selected="true">index (1-based) in MGF</option> 295 <option value="1">index (1-based) in MGF</option>
273 <option value="2">spectrum title in MGF</option> 296 <option value="2">spectrum title in MGF</option>
274 </param> 297 </param>
275 </section> 298 </section>
276 299
277 <param name="parameter_set" argument="-p" type="text" value="" optional="true" label="MS/MS searching parameter set name"> 300 <param name="parameter_set" argument="-p" type="text" value="" optional="true" label="MS/MS searching parameter set name">
287 <option value="TMT10_11_ubiquitination">TMT10_11_ubiquitination</option> 310 <option value="TMT10_11_ubiquitination">TMT10_11_ubiquitination</option>
288 </param> 311 </param>
289 312
290 <section name="modifications" title="Modifications" expanded="false"> 313 <section name="modifications" title="Modifications" expanded="false">
291 <param name="fixed_mod" argument="-fixMod" type="select" label="Fixed modification(s)" multiple="true" optional="true"> 314 <param name="fixed_mod" argument="-fixMod" type="select" label="Fixed modification(s)" multiple="true" optional="true">
292 <help>default: 1: Carbamidomethylation of C [57.02146372057]</help> 315 <help>Default: 1: Carbamidomethylation of C [57.02146372057]</help>
293 <expand macro="modifications" /> 316 <expand macro="modifications" />
294 </param> 317 </param>
295 <param name="var_mod" argument="-varMod" type="select" label="Variable modification(s)" multiple="true" optional="true"> 318 <param name="var_mod" argument="-varMod" type="select" label="Variable modification(s)" multiple="true" optional="true">
296 <help>default: 2: Oxidation of M [15.99491461956]</help> 319 <help>Default: 2: Oxidation of M [15.99491461956]</help>
297 <expand macro="modifications" /> 320 <expand macro="modifications" />
298 </param> 321 </param>
299 322
300 <param name="max_mods" argument="-maxVar" type="integer" label="Max Modifications" value="" min="0" max="10" optional="true" help="Max number of variable modifications Default: 3" /> 323 <param name="max_mods" argument="-maxVar" type="integer" label="Max Modifications" value="" min="0" max="10" optional="true" help="Max number of variable modifications Default: 3" />
301 <param name="unmodified" argument="-hc" type="boolean" truevalue="-hc" falsevalue="" checked="false" label="Use more stringent criterion for unrestricted modification searching" help="TRUE: score(UMS)>=score(targetPSM); FALSE: score(UMS)>score(targetPSM)" /> 324 <param name="unmodified" argument="-hc" type="boolean" truevalue="-hc" falsevalue="" checked="false" label="Use more stringent criterion for unrestricted modification searching" help="TRUE: score(UMS)>=score(targetPSM); FALSE: score(UMS)>score(targetPSM)" />
302 <param name="aa" argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." /> 325 <param name="aa" argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." />
303 </section> 326 </section>
304 327
305 <section name="digestion" title="Digestion" expanded="false"> 328 <section name="digestion" title="Digestion" expanded="false">
306 <param name="enzyme" argument="-e" type="select" optional="true" label="Enzyme" help="Enzyme used for protein digestion" > 329 <param name="enzyme" argument="-e" type="select" optional="true" label="Enzyme" help="Enzyme used for protein digestion. Default: Trypsin" >
307 <option value="0">Non enzyme</option> 330 <option value="0">Non enzyme</option>
308 <option value="1" selected="true">Trypsin</option> 331 <option value="1">Trypsin</option>
309 <option value="2">Trypsin (no P rule)</option> 332 <option value="2">Trypsin (no P rule)</option>
310 <option value="3">Arg-C</option> 333 <option value="3">Arg-C</option>
311 <option value="4">Arg-C (no P rule)</option> 334 <option value="4">Arg-C (no P rule)</option>
312 <option value="5">Arg-N</option> 335 <option value="5">Arg-N</option>
313 <option value="6">Glu-C</option> 336 <option value="6">Glu-C</option>
317 </section> 340 </section>
318 341
319 <section name="ms_params" title="Mass spectrometer" expanded="false"> 342 <section name="ms_params" title="Mass spectrometer" expanded="false">
320 <section name="tolerance_params" title="Tolerance" expanded="true"> 343 <section name="tolerance_params" title="Tolerance" expanded="true">
321 <param name="precursor_tolerance" argument="-tol" type="integer" value="" optional="true" label="Precursor Tolerance" help="The error window on experimental peptide mass values. This parameter is usually set according to the mass spectrometer which was used to generate the MS/MS data. Default: 10" /> 344 <param name="precursor_tolerance" argument="-tol" type="integer" value="" optional="true" label="Precursor Tolerance" help="The error window on experimental peptide mass values. This parameter is usually set according to the mass spectrometer which was used to generate the MS/MS data. Default: 10" />
322 <param name="precursor_unit" argument="-tolu" type="select" optional="true" label="Precursor Unit" help="The unit of precursor ion m/z tolerance"> 345 <param name="precursor_unit" argument="-tolu" type="select" optional="true" label="Precursor Unit" help="The unit of precursor ion m/z tolerance. Default: ppm">
323 <option value="ppm" selected="true">ppm</option> 346 <option value="ppm">ppm</option>
324 <option value="Da">Da</option> 347 <option value="Da">Da</option>
325 </param> 348 </param>
326 <param name="tolerance" argument="-itol" type="float" value="" optional="true" label="Tolerance" help="Error window for MS/MS fragment ion mass values in Da unit. Default: 0.6 Da" /> 349 <param name="tolerance" argument="-itol" type="float" value="" optional="true" label="Tolerance" help="Error window for MS/MS fragment ion mass values in Da unit. Default: 0.6 Da" />
327 </section> 350 </section>
328 351
329 <section name="search" title="PSM" expanded="false"> 352 <section name="search" title="PSM" expanded="false">
330 <param name="frag_method" argument="-fragmentMethod" type="select" optional="true" label="Fragmentation Method"> 353 <param name="frag_method" argument="-fragmentMethod" type="select" optional="true" label="Fragmentation Method" help="Default: CID/HCD">
331 <option value="1" selected="true">CID/HCD</option> 354 <option value="1">CID/HCD</option>
332 <option value="2">ETD</option> 355 <option value="2">ETD</option>
333 </param> 356 </param>
334 <param name="scoring_method" argument="-m" type="select" optional="true" label="Scoring Method"> 357 <param name="scoring_method" argument="-m" type="select" optional="true" label="Scoring Method" help="Default: HyperScore">
335 <option value="1" selected="true">HyperScore</option> 358 <option value="1">HyperScore</option>
336 <option value="2">MVH</option> 359 <option value="2">MVH</option>
337 </param> 360 </param>
338 <param name="extra_score_validation" argument="-x" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Add extra score validation" help="use two scoring algorithms for peptide identification" /> 361 <param name="extra_score_validation" argument="-x" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Add extra score validation" help="use two scoring algorithms for peptide identification" />
339 <param name="min_charge" argument="-minCharge" type="integer" value="" optional="true" label="Minimum Charge" help="The minimum charge to consider if the charge state is not available. Default: 2"/> 362 <param name="min_charge" argument="-minCharge" type="integer" value="" optional="true" label="Minimum Charge" help="The minimum charge to consider if the charge state is not available. Default: 2"/>
340 <param name="max_charge" argument="-maxCharge" type="integer" value="" optional="true" label="Maximum Charge" help="The maximum charge to consider if the charge state is not available. Default: 3" /> 363 <param name="max_charge" argument="-maxCharge" type="integer" value="" optional="true" label="Maximum Charge" help="The maximum charge to consider if the charge state is not available. Default: 3" />
357 <option value="psm_annotation.txt" selected="true">psm_annotation.txt</option> 380 <option value="psm_annotation.txt" selected="true">psm_annotation.txt</option>
358 <option value="psm_type.txt" selected="false">psm_type.txt</option> 381 <option value="psm_type.txt" selected="false">psm_type.txt</option>
359 <option value="detail.txt" selected="true">detail.txt</option> 382 <option value="detail.txt" selected="true">detail.txt</option>
360 <option value="ptm.txt" selected="true">ptm.txt</option> 383 <option value="ptm.txt" selected="true">ptm.txt</option>
361 <option value="ptm_detail.txt" selected="true">ptm_detail.txt</option> 384 <option value="ptm_detail.txt" selected="true">ptm_detail.txt</option>
362 <option value="ptm_detail.txt" selected="true">ptm_detail.txt</option>
363 <option value="ms_index" selected="true">MS/MS Index</option> 385 <option value="ms_index" selected="true">MS/MS Index</option>
364 </param> 386 </param>
365 <param name="fast" argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." /> 387 <param name="fast" argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." />
366 </inputs> 388 </inputs>
367 <outputs> 389 <outputs>
390 <data name="log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt">
391 </data>
368 <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt"> 392 <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt">
369 </data> 393 </data>
370 <data name="ms_index" format="txt" label="${tool.name} on ${on_string}: index summary.txt" from_work_dir="index_dir/summary.txt"> 394 <data name="ms_index" format="txt" label="${tool.name} on ${on_string}: index summary.txt" from_work_dir="index_dir/summary.txt">
371 <filter>'ms_index' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter> 395 <filter>'ms_index' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter>
372 </data> 396 </data>