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comparison pepquery2.xml @ 2:c32806a80862 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 22916ed24dfb8452c8142e5d6b282d0e931af91f
author galaxyp
date Wed, 08 May 2024 17:12:21 +0000
parents b5489f81c2fa
children
comparison
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1:b5489f81c2fa 2:c32806a80862
157 <option value="novel" selected="true">novel peptide/protein validation</option> 157 <option value="novel" selected="true">novel peptide/protein validation</option>
158 <option value="known">known peptide/protein validation</option> 158 <option value="known">known peptide/protein validation</option>
159 </param> 159 </param>
160 <when value="novel"/> 160 <when value="novel"/>
161 <when value="known"> 161 <when value="known">
162 <param name="decoy" argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/> 162 <param argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/>
163 </when> 163 </when>
164 </conditional> 164 </conditional>
165 <section name="req_inputs" title="Input Data" expanded="true"> 165 <section name="req_inputs" title="Input Data" expanded="true">
166 <conditional name="input_type"> 166 <conditional name="input_type">
167 <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" > 167 <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" >
255 <option value="indexed">Indexed MS/MS spectrums</option> 255 <option value="indexed">Indexed MS/MS spectrums</option>
256 <option value="PepQueryDB">PepQueryDB</option> 256 <option value="PepQueryDB">PepQueryDB</option>
257 <option value="public">public proteomics data repositories</option> 257 <option value="public">public proteomics data repositories</option>
258 </param> 258 </param>
259 <when value="history"> 259 <when value="history">
260 <param name="spectrum_files" argument="-ms" type="data" format="mgf,mzml,mzxml,thermo.raw" label="Spectrum File" help="Spectrum file used for identification, formats: MGF,mzML,mzXML,Thermo RAW" /> 260 <param name="spectrum_files" argument="-ms" type="data" format="mgf,mzml,mzxml" label="Spectrum File" help="Spectrum file used for identification, formats: MGF,mzML,mzXML" />
261 </when> 261 </when>
262 <when value="indexed"> 262 <when value="indexed">
263 <param name="index" argument="-ms" type="data" format="txt" label="PepQuery Index" help="" /> 263 <param name="index" argument="-ms" type="data" format="txt" label="PepQuery Index" help="" />
264 </when> 264 </when>
265 <when value="PepQueryDB"> 265 <when value="PepQueryDB">
274 <validator type="regex" message="An identifier strating with PXD or MSV or JPST">^(PXD|MSV|JPST).*$</validator> 274 <validator type="regex" message="An identifier strating with PXD or MSV or JPST">^(PXD|MSV|JPST).*$</validator>
275 </param> 275 </param>
276 </when> 276 </when>
277 </conditional> 277 </conditional>
278 278
279 <param name="indexType" argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" > 279 <param argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" >
280 <option value="1">index (1-based) in MGF</option> 280 <option value="1">index (1-based) in MGF</option>
281 <option value="2">spectrum title in MGF</option> 281 <option value="2">spectrum title in MGF</option>
282 </param> 282 </param>
283 </section> 283 </section>
284 284
305 <expand macro="modifications" /> 305 <expand macro="modifications" />
306 </param> 306 </param>
307 307
308 <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" /> 308 <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" />
309 <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)" /> 309 <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)" />
310 <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." /> 310 <param 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." />
311 </section> 311 </section>
312 312
313 <section name="digestion" title="Digestion" expanded="false"> 313 <section name="digestion" title="Digestion" expanded="false">
314 <param name="enzyme" argument="-e" type="select" optional="true" label="Enzyme" help="Enzyme used for protein digestion. Default: Trypsin" > 314 <param name="enzyme" argument="-e" type="select" optional="true" label="Enzyme" help="Enzyme used for protein digestion. Default: Trypsin" >
315 <option value="0">Non enzyme</option> 315 <option value="0">Non enzyme</option>
367 <option value="detail.txt">detail.txt</option> 367 <option value="detail.txt">detail.txt</option>
368 <option value="ptm.txt">ptm.txt</option> 368 <option value="ptm.txt">ptm.txt</option>
369 <option value="ptm_detail.txt">ptm_detail.txt</option> 369 <option value="ptm_detail.txt">ptm_detail.txt</option>
370 <option value="ms_index">MS/MS Index</option> 370 <option value="ms_index">MS/MS Index</option>
371 </param> 371 </param>
372 <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." /> 372 <param 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." />
373 </inputs> 373 </inputs>
374 <outputs> 374 <outputs>
375 <data name="log_txt" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt"> 375 <data name="log_txt" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt">
376 </data> 376 </data>
377 <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt"> 377 <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt">