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comparison peptide_shaker.xml @ 53:d67a3c1bfd09 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424
author galaxyp
date Wed, 08 May 2019 14:06:07 -0400
parents 864bd76db767
children 7fdd9119cc4f
comparison
equal deleted inserted replaced
52:864bd76db767 53:d67a3c1bfd09
1 <tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@.2"> 1 <tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@.3">
2 <description> 2 <description>
3 Perform protein identification using various search engines based on results from SearchGUI 3 Perform protein identification using various search engines based on results from SearchGUI
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
127 -out_reports \$cwd/output_reports 127 -out_reports \$cwd/output_reports
128 -reports #echo ','.join($output_reports_list)# 128 -reports #echo ','.join($output_reports_list)#
129 #end if 129 #end if
130 130
131 2>> $temp_stderr) 131 2>> $temp_stderr)
132
133 ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them
134 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip:
135 && unzip \$cwd/peptideshaker_output.zip 'reports/*' -d \$cwd/output_reports
136 #end if
132 137
133 #if len(output_reports_list)>0: 138 #if len(output_reports_list)>0:
134 #if '0' in $output_reports_list: 139 #if '0' in $output_reports_list:
135 && find \$cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \; 140 && find \$cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
136 #end if 141 #end if
285 <conditional name="zip_conditional"> 290 <conditional name="zip_conditional">
286 <param name="zip_output_boolean" type="boolean" truevalue="zip" falsevalue="separate" checked="false" label="Compress results into a single zip file" /> 291 <param name="zip_output_boolean" type="boolean" truevalue="zip" falsevalue="separate" checked="false" label="Compress results into a single zip file" />
287 <when value="separate"> 292 <when value="separate">
288 <param name="export_cps" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Exports the CPS file" /> 293 <param name="export_cps" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Exports the CPS file" />
289 </when> 294 </when>
290 <when value="zip" /> 295 <when value="zip">
296 <param name="export_reports_when_zip" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Also export reports out of the zip" />
297 </when>
291 </conditional> 298 </conditional>
292 299
293 <param name="output_reports" type="select" display="checkboxes" multiple="True" optional="true" label="Reports to be generated"> 300 <param name="output_reports" type="select" display="checkboxes" multiple="True" optional="true" label="Reports to be generated">
294 <option value="3">PSM Report</option> 301 <option value="3">PSM Report</option>
295 <option value="4">PSM Report with non-validated matches</option> 302 <option value="4">PSM Report with non-validated matches</option>
308 </section> 315 </section>
309 316
310 </inputs> 317 </inputs>
311 <outputs> 318 <outputs>
312 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file"> 319 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
313 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and mzidentml_conditional['mzidentml_creation'] is True</filter> 320 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['mzidentml_conditional']['mzidentml_creation'] is True</filter>
314 </data> 321 </data>
315 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file"> 322 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file">
316 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['zip_conditional']['export_cps'] is True</filter> 323 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['zip_conditional']['export_cps'] is True</filter>
317 </data> 324 </data>
318 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive"> 325 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
322 <data format="tabular" name="reports"> 329 <data format="tabular" name="reports">
323 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="output_reports" visible="true" assign_primary_output="true" /> 330 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="output_reports" visible="true" assign_primary_output="true" />
324 </data> 331 </data>
325 --> 332 -->
326 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters"> 333 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
327 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '0' in exporting_options['output_reports']</filter> 334 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '0' in exporting_options['output_reports']</filter>
328 </data> 335 </data>
329 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report"> 336 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
330 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '1' in exporting_options['output_reports']</filter> 337 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '1' in exporting_options['output_reports']</filter>
331 </data> 338 </data>
332 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report"> 339 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
333 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '2' in exporting_options['output_reports']</filter> 340 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '2' in exporting_options['output_reports']</filter>
334 </data> 341 </data>
335 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report"> 342 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
336 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '3' in exporting_options['output_reports']</filter> 343 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '3' in exporting_options['output_reports']</filter>
337 </data> 344 </data>
338 <data format="tabular" name="output_psm_nonvalidated" from_work_dir="psm_nonvalidated.txt" label="${tool.name} on ${on_string}: PSM Report with non-validated matches"> 345 <data format="tabular" name="output_psm_nonvalidated" from_work_dir="psm_nonvalidated.txt" label="${tool.name} on ${on_string}: PSM Report with non-validated matches">
339 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '4' in exporting_options['output_reports']</filter> 346 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '4' in exporting_options['output_reports']</filter>
340 </data> 347 </data>
341 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report"> 348 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
342 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '11' in exporting_options['output_reports']</filter> 349 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '11' in exporting_options['output_reports']</filter>
343 </data> 350 </data>
344 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report"> 351 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
345 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '5' in exporting_options['output_reports']</filter> 352 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '5' in exporting_options['output_reports']</filter>
346 </data> 353 </data>
347 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report"> 354 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
348 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '6' in exporting_options['output_reports']</filter> 355 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '6' in exporting_options['output_reports']</filter>
349 </data> 356 </data>
350 <data format="tabular" name="output_peptides_nonvalidated" from_work_dir="peptides_nonvalidated.txt" label="${tool.name} on ${on_string}: Peptide Report with non-validated matches"> 357 <data format="tabular" name="output_peptides_nonvalidated" from_work_dir="peptides_nonvalidated.txt" label="${tool.name} on ${on_string}: Peptide Report with non-validated matches">
351 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '7' in exporting_options['output_reports']</filter> 358 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '7' in exporting_options['output_reports']</filter>
352 </data> 359 </data>
353 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report"> 360 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
354 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '8' in exporting_options['output_reports']</filter> 361 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '8' in exporting_options['output_reports']</filter>
355 </data> 362 </data>
356 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report"> 363 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
357 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '9' in exporting_options['output_reports']</filter> 364 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '9' in exporting_options['output_reports']</filter>
358 </data> 365 </data>
359 <data format="tabular" name="output_proteins_nonvalidated" from_work_dir="proteins_nonvalidated.txt" label="${tool.name} on ${on_string}: Protein Repor with non-validated matches"> 366 <data format="tabular" name="output_proteins_nonvalidated" from_work_dir="proteins_nonvalidated.txt" label="${tool.name} on ${on_string}: Protein Repor with non-validated matches">
360 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '10' in exporting_options['output_reports']</filter> 367 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '10' in exporting_options['output_reports']</filter>
361 </data> 368 </data>
362 </outputs> 369 </outputs>
363 <tests> 370 <tests>
364 <test> 371 <test expect_num_outputs="1">
365 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/> 372 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
366 <param name="processing_options_selector" value="no"/> 373 <param name="processing_options_selector" value="no"/>
367 <param name="filtering_options_selector" value="no"/> 374 <param name="filtering_options_selector" value="no"/>
368 <param name="mzidentml_creation" value="0"/> 375 <param name="mzidentml_creation" value="0"/>
369 <param name="zip_output_boolean" value="zip"/> 376 <param name="zip_output_boolean" value="zip"/>
370 <param name="export_cps" value="1"/> 377 <param name="export_cps" value="1"/>
371 <output name="output_zip" file="peptide_shaker_modifications_result1.zip" ftype="zip" compare="sim_size" delta="3000" /> 378 <output name="output_zip" file="peptide_shaker_modifications_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
372 </test> 379 </test>
373 <test> 380 <test expect_num_outputs="12">
374 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/> 381 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
375 <param name="processing_options_selector" value="no"/> 382 <param name="processing_options_selector" value="no"/>
376 <param name="filtering_options_selector" value="yes"/> 383 <param name="filtering_options_selector" value="yes"/>
377 <param name="min_peptide_length" value="1"/> 384 <param name="min_peptide_length" value="1"/>
378 <param name="mzidentml_creation" value="0"/> 385 <param name="mzidentml_creation" value="0"/>
389 <output name="output_peptides_nonvalidated" file="peptide_shaker_modifications_result1.output_peptides_nonvalidated" ftype="tabular"/> 396 <output name="output_peptides_nonvalidated" file="peptide_shaker_modifications_result1.output_peptides_nonvalidated" ftype="tabular"/>
390 <output name="output_proteins" file="peptide_shaker_modifications_result1.output_proteins" ftype="tabular"/> 397 <output name="output_proteins" file="peptide_shaker_modifications_result1.output_proteins" ftype="tabular"/>
391 <output name="output_proteins_phosphorylation" file="peptide_shaker_modifications_result1.output_proteins_phosphorylation" ftype="tabular"/> 398 <output name="output_proteins_phosphorylation" file="peptide_shaker_modifications_result1.output_proteins_phosphorylation" ftype="tabular"/>
392 <output name="output_proteins_nonvalidated" file="peptide_shaker_modifications_result1.output_proteins_nonvalidated" ftype="tabular"/> 399 <output name="output_proteins_nonvalidated" file="peptide_shaker_modifications_result1.output_proteins_nonvalidated" ftype="tabular"/>
393 </test> 400 </test>
394 <test> 401 <test expect_num_outputs="2">
395 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/> 402 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
396 <param name="processing_options_selector" value="no"/> 403 <param name="processing_options_selector" value="no"/>
397 <param name="filtering_options_selector" value="no"/> 404 <param name="filtering_options_selector" value="no"/>
398 <param name="mzidentml_creation" value="0"/> 405 <param name="mzidentml_creation" value="0"/>
399 <param name="zip_output_boolean" value="separate"/> 406 <param name="zip_output_boolean" value="separate"/>