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comparison pepquery2.xml @ 3:d8962e547c9c draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
author galaxyp
date Tue, 25 Oct 2022 23:35:01 +0000
parents 3b2874c58bcd
children 29e6417b913c
comparison
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2:3b2874c58bcd 3:d8962e547c9c
176 <param name="peptide_input_selector" type="select" label="Peptides?"> 176 <param name="peptide_input_selector" type="select" label="Peptides?">
177 <option value="multiple">Peptide list from your history</option> 177 <option value="multiple">Peptide list from your history</option>
178 <option value="single">Single peptide entered as text</option> 178 <option value="single">Single peptide entered as text</option>
179 </param> 179 </param>
180 <when value="multiple"> 180 <when value="multiple">
181 <param name="input" argument="-i" type="data" format="txt" label="Peptide Sequences (.txt)"> 181 <param name="input" argument="-i" type="data" format="tabular" label="Peptide Sequences (.txt)">
182 <help>Peptide sequence file containing peptides which you want to search (no column headers). 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. 183 First column is am peptide sequence. Optional second column is spectrum title.
184 </help> 184 </help>
185 </param> 185 </param>
186 </when> 186 </when>
187 <when value="single"> 187 <when value="single">
188 <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">
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]+)*$</validator> 189 <validator type="regex" message="Must be AA letters, multiple peptides separated by commas">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+(,[AC-IK-NP-TV-Yac-ik-np-tv-y]+)*$</validator>
190 </param> 190 </param>
191 </when> 191 </when>
192 </conditional> 192 </conditional>
193 </when> 193 </when>
194 <when value="protein"> 194 <when value="protein">
385 <option value="ms_index" selected="true">MS/MS Index</option> 385 <option value="ms_index" selected="true">MS/MS Index</option>
386 </param> 386 </param>
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." /> 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." />
388 </inputs> 388 </inputs>
389 <outputs> 389 <outputs>
390 <data name="log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt"> 390 <data name="log_txt" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt">
391 </data> 391 </data>
392 <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${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 ${on_string}: parameter.txt">
393 </data> 393 </data>
394 <data name="ms_index" format="txt" label="${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">
395 <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>
460 <section name="req_inputs"> 460 <section name="req_inputs">
461 <conditional name="input_type"> 461 <conditional name="input_type">
462 <param name="input_type_selector" value="peptide"/> 462 <param name="input_type_selector" value="peptide"/>
463 <conditional name="multiple"> 463 <conditional name="multiple">
464 <param name="peptide_input_selector" value="single" /> 464 <param name="peptide_input_selector" value="single" />
465 <param name="input" value="LVVVGADGVGK"/> 465 <param name="input" value="LVVVGADGVGK,AHSSMVGVNLPQK"/>
466 </conditional> 466 </conditional>
467 </conditional> 467 </conditional>
468 <conditional name="db_type"> 468 <conditional name="db_type">
469 <param name="db_type_selector" value="download" /> 469 <param name="db_type_selector" value="download" />
470 <param name="db_id" value="gencode:human"/> 470 <param name="db_id" value="gencode:human"/>
508 </section> 508 </section>
509 </section> 509 </section>
510 <output name="psm_txt"> 510 <output name="psm_txt">
511 <assert_contents> 511 <assert_contents>
512 <has_text text="LVVVGADGVGK" /> 512 <has_text text="LVVVGADGVGK" />
513 <not_has_text text="AHSSMVGVNLPQK" />
513 <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" /> 514 <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
514 </assert_contents> 515 </assert_contents>
515 </output> 516 </output>
517 <output name="log_txt">
518 <assert_contents>
519 <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" />
520 </assert_contents>
521 </output>
516 </test> 522 </test>
517 523
518 <!-- Test-2 MGF peptide Uniprot.fasta --> 524 <!-- Test-2 PepQueryDB peptide gencode:human pep.txt -->
519 <test> 525 <test>
520 <conditional name="validation"> 526 <conditional name="validation">
521 <param name="task_type" value="novel"/> 527 <param name="task_type" value="novel"/>
522 </conditional> 528 </conditional>
523 <section name="req_inputs"> 529 <section name="req_inputs">
524 <conditional name="input_type"> 530 <conditional name="input_type">
525 <param name="input_type_selector" value="peptide"/> 531 <param name="input_type_selector" value="peptide"/>
526 <conditional name="multiple"> 532 <conditional name="multiple">
527 <param name="peptide_input_selector" value="single" /> 533 <param name="peptide_input_selector" value="multiple" />
528 <param name="input" value="ELGSSDLTAR"/> 534 <param name="input" ftype="tabular" value="pep.txt"/>
529 </conditional> 535 </conditional>
530 </conditional> 536 </conditional>
531 <conditional name="db_type"> 537 <conditional name="db_type">
532 <param name="db_type_selector" value="history" /> 538 <param name="db_type_selector" value="download" />
533 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/> 539 <param name="db_id" value="gencode:human"/>
534 </conditional> 540 </conditional>
535 <conditional name="ms_dataset"> 541 <conditional name="ms_dataset">
536 <param name="ms_dataset_type" value="history"/> 542 <param name="ms_dataset_type" value="PepQueryDB"/>
537 <param name="spectrum_files" ftype="mgf" value="iTRAQ_f4.mgf"/> 543 <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" />
538 </conditional> 544 </conditional>
539 <param name="indexType" value="1"/> 545 <param name="indexType" value="1"/>
540 </section> 546 </section>
541 <param name="parameter_set" value=""/> 547 <param name="parameter_set" value=""/>
542 <section name="modifications"> 548 <section name="modifications">
543 <!-- 21: iTRAQ 4-plex of K [144.1020624208] --> 549 <param name="fixed_mod" value="1"/>
544 <!-- 22: iTRAQ 4-plex of peptide N-term [144.1020624208] -->
545 <param name="fixed_mod" value="1,21,22"/>
546 <!-- 2: Oxidation of M [15.99491461956] -->
547 <param name="var_mod" value="2"/> 550 <param name="var_mod" value="2"/>
548 <param name="max_mods" value="3"/> 551 <param name="max_mods" value="3"/>
549 <param name="unmodified" value="True"/> 552 <param name="unmodified" value="True"/>
550 <param name="aa" value="False"/> 553 <param name="aa" value="False"/>
551 </section> 554 </section>
573 <param name="num_random_peptides" value="1000"/> 576 <param name="num_random_peptides" value="1000"/>
574 </section> 577 </section>
575 </section> 578 </section>
576 <output name="psm_txt"> 579 <output name="psm_txt">
577 <assert_contents> 580 <assert_contents>
581 <has_text text="LVVVGADGVGK" />
582 <not_has_text text="AHSSMVGVNLPQK" />
583 <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
584 </assert_contents>
585 </output>
586 <output name="log_txt">
587 <assert_contents>
588 <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" />
589 </assert_contents>
590 </output>
591 </test>
592
593 <!-- Test-3 MGF peptide Uniprot.fasta -->
594 <test>
595 <conditional name="validation">
596 <param name="task_type" value="novel"/>
597 </conditional>
598 <section name="req_inputs">
599 <conditional name="input_type">
600 <param name="input_type_selector" value="peptide"/>
601 <conditional name="multiple">
602 <param name="peptide_input_selector" value="single" />
603 <param name="input" value="ELGSSDLTAR"/>
604 </conditional>
605 </conditional>
606 <conditional name="db_type">
607 <param name="db_type_selector" value="history" />
608 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
609 </conditional>
610 <conditional name="ms_dataset">
611 <param name="ms_dataset_type" value="history"/>
612 <param name="spectrum_files" ftype="mgf" value="iTRAQ_f4.mgf"/>
613 </conditional>
614 <param name="indexType" value="1"/>
615 </section>
616 <param name="parameter_set" value=""/>
617 <section name="modifications">
618 <!-- 21: iTRAQ 4-plex of K [144.1020624208] -->
619 <!-- 22: iTRAQ 4-plex of peptide N-term [144.1020624208] -->
620 <param name="fixed_mod" value="1,21,22"/>
621 <!-- 2: Oxidation of M [15.99491461956] -->
622 <param name="var_mod" value="2"/>
623 <param name="max_mods" value="3"/>
624 <param name="unmodified" value="True"/>
625 <param name="aa" value="False"/>
626 </section>
627 <section name="digestion">
628 <param name="enzyme" value="1"/>
629 <param name="max_missed_cleavages" value="2"/>
630 </section>
631 <section name="ms_params">
632 <section name="tolerance_params">
633 <param name="precursor_tolerance" value="10"/>
634 <param name="precursor_unit" value="ppm"/>
635 <param name="tolerance" value="0.6"/>
636 </section>
637 <section name="search">
638 <param name="frag_method" value="1"/>
639 <param name="scoring_method" value="1"/>
640 <param name="extra_score_validation" value="False"/>
641 <param name="min_charge" value="2"/>
642 <param name="max_charge" value="3"/>
643 <param name="min_peaks" value="10"/>
644 <param name="isotope_error" value="0"/>
645 <param name="min_score" value="12"/>
646 <param name="min_length" value="7"/>
647 <param name="max_length" value="45"/>
648 <param name="num_random_peptides" value="1000"/>
649 </section>
650 </section>
651 <output name="psm_txt">
652 <assert_contents>
578 <has_text text="ELGSSDLTAR" /> 653 <has_text text="ELGSSDLTAR" />
579 </assert_contents> 654 </assert_contents>
580 </output> 655 </output>
581 <output name="psm_rank_txt"> 656 <output name="psm_rank_txt">
582 <assert_contents> 657 <assert_contents>
584 <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\[144.1\d+\]\t2\tiTRAQ_f4:3:2\t2\t1191.62\d+\t-3.04\d+\t-0.003\d+\t0.0\t1191.6\d+\t596.8\d+\t24.1\d+\t0\t0\t1\t995\t0.002\d+\t1\t0\tYes\t24.1\d+\t24.1\d+"/> 659 <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\[144.1\d+\]\t2\tiTRAQ_f4:3:2\t2\t1191.62\d+\t-3.04\d+\t-0.003\d+\t0.0\t1191.6\d+\t596.8\d+\t24.1\d+\t0\t0\t1\t995\t0.002\d+\t1\t0\tYes\t24.1\d+\t24.1\d+"/>
585 </assert_contents> 660 </assert_contents>
586 </output> 661 </output>
587 </test> 662 </test>
588 663
664 <!-- Test-4 PepQueryDB known peptide gencode:human pep.txt -->
665 <test>
666 <conditional name="validation">
667 <param name="task_type" value="known"/>
668 </conditional>
669 <section name="req_inputs">
670 <conditional name="input_type">
671 <param name="input_type_selector" value="peptide"/>
672 <conditional name="multiple">
673 <param name="peptide_input_selector" value="single" />
674 <param name="input" value="AHSSMVGVNLPQK"/>
675 </conditional>
676 </conditional>
677 <conditional name="db_type">
678 <param name="db_type_selector" value="download" />
679 <param name="db_id" value="gencode:human"/>
680 </conditional>
681 <conditional name="ms_dataset">
682 <param name="ms_dataset_type" value="PepQueryDB"/>
683 <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" />
684 </conditional>
685 <param name="indexType" value="1"/>
686 </section>
687 <section name="modifications">
688 <param name="unmodified" value="True"/>
689 </section>
690 <output name="psm_txt">
691 <assert_contents>
692 <has_text text="AHSSMVGVNLPQK" />
693 <has_text text="6CPTAC_LUAD_W_BI_20180718_KL_f12:20286:3" />
694 </assert_contents>
695 </output>
696 </test>
697
589 </tests> 698 </tests>
590 <help><![CDATA[ 699 <help><![CDATA[
591 **PepQuery2** 700 **PepQuery2**
592 701
593 PepQuery_ is a universal targeted peptide search engine for identifying or validating known and novel peptides of interest in any local or publicly available mass spectrometry-based proteomics datasets. 702 PepQuery_ is a universal targeted peptide search engine for identifying or validating known and novel peptides of interest in any local or publicly available mass spectrometry-based proteomics datasets.