Mercurial > repos > galaxyp > peptideshaker

comparison peptide_shaker.xml @ 32:ff592231f118 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
author galaxyp
date Wed, 25 Jan 2017 15:37:43 -0500
parents ad60446b1e93
children bce45e9e6d70
comparison
equal deleted inserted replaced
31:f3f67aa3123b 32:ff592231f118
335 <test> 335 <test>
336 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> 336 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
337 <param name="processing_options_selector" value="no"/> 337 <param name="processing_options_selector" value="no"/>
338 <param name="filtering_options_selector" value="no"/> 338 <param name="filtering_options_selector" value="no"/>
339 <param name="outputs" value="zip,3"/> 339 <param name="outputs" value="zip,3"/>
340 <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="600" /> 340 <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="900" />
341 <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" /> 341 <output name="output_psm">
342 <assert_contents>
343 <has_text text="cds.comp41779_c0_seq1" />
344 </assert_contents>
345 </output>
342 </test> 346 </test>
343 <test> 347 <test>
344 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> 348 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
345 <param name="processing_options_selector" value="no"/> 349 <param name="processing_options_selector" value="no"/>
346 <param name="filtering_options_selector" value="yes"/> 350 <param name="filtering_options_selector" value="yes"/>
347 <param name="min_peptide_length" value="1"/> 351 <param name="min_peptide_length" value="1"/>
348 <param name="outputs" value="0,1,2,3,4,5,6,7"/> 352 <param name="outputs" value="0,1,2,3,4,5,6,7"/>
349 <output name="output_certificate" file="peptide_shaker_certificate_result2.txt" ftype="txt" lines_diff="6"/> 353 <output name="output_certificate">
350 <output name="output_hierarchical" file="peptide_shaker_hierarchical_result2.tabular" ftype="tabular" /> 354 <assert_contents>
351 <output name="output_psm" file="peptide_shaker_psm_result2.tabular" ftype="tabular" /> 355 <has_text text="Tolerance: 100" />
352 <output name="output_psm_phosphorylation" file="peptide_shaker_psm_phoshorylation_result2.tabular" ftype="tabular" /> 356 <has_text text="Carbamidomethylation of C" />
353 <output name="output_peptides" file="peptide_shaker_peptides_result2.tabular" ftype="tabular" /> 357 </assert_contents>
354 <output name="output_peptides_phosphorylation" file="peptide_shaker_peptides_phoshorylation_result2.tabular" ftype="tabular" /> 358 </output>
355 <output name="output_proteins" file="peptide_shaker_proteins_result2.tabular" ftype="tabular" /> 359 <output name="output_hierarchical">
356 <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" /> 360 <assert_contents>
361 <has_text_matching expression="1.1\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2" />
362 </assert_contents>
363 </output>
364 <output name="output_psm">
365 <assert_contents>
366 <not_has_text text="Phosphosite" />
367 <has_text text="cds.comp41779_c0_seq1" />
368 </assert_contents>
369 </output>
370 <output name="output_psm_phosphorylation">
371 <assert_contents>
372 <has_text text="Phosphosite" />
373 <has_text text="cds.comp41779_c0_seq1" />
374 </assert_contents>
375 </output>
376 <output name="output_peptides">
377 <assert_contents>
378 <has_text text="Modification" />
379 <has_text text="cds.comp41779_c0_seq1" />
380 </assert_contents>
381 </output>
382 <output name="output_peptides_phosphorylation">
383 <assert_contents>
384 <has_text text="Phosphosite" />
385 <has_text text="cds.comp41779_c0_seq1" />
386 </assert_contents>
387 </output>
388 <output name="output_proteins">
389 <assert_contents>
390 <has_text text="Modification" />
391 <has_text text="cds.comp41779_c0_seq1" />
392 </assert_contents>
393 </output>
394 <output name="output_proteins_phosphorylation">
395 <assert_contents>
396 <has_text text="Phosphosite" />
397 <has_text text="cds.comp41779_c0_seq1" />
398 </assert_contents>
399 </output>
357 </test> 400 </test>
358 </tests> 401 </tests>
359 <help> 402 <help>
360 **What it does** 403 **What it does**
361 404