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comparison pepquery2.xml @ 6:01fd80b15053 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
author galaxyp
date Sun, 06 Nov 2022 16:23:05 +0000
parents 2045f3b68773
children
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5:2045f3b68773 6:01fd80b15053
163 <conditional name="input_type"> 163 <conditional name="input_type">
164 <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="" >
165 <option value="peptide">peptide</option> 165 <option value="peptide">peptide</option>
166 <option value="protein">protein</option> 166 <option value="protein">protein</option>
167 <option value="DNA">DNA (translate to protein sequences)</option> 167 <option value="DNA">DNA (translate to protein sequences)</option>
168 <!-- these are not working with pepquery version 1.6 168 <!-- VCF,BED,GTF input options have not been implemented in this tool -->
169 <option value="3">VCF (translate to protein sequences)</option>
170 <option value="4">BED (translate to protein sequences)</option>
171 <option value="5">GTF (translate to protein sequences)</option>
172 -->
173 </param> 169 </param>
174 <when value="peptide"> 170 <when value="peptide">
175 <conditional name="multiple"> 171 <conditional name="multiple">
176 <param name="peptide_input_selector" type="select" label="Peptides?"> 172 <param name="peptide_input_selector" type="select" label="Peptides?">
177 <option value="multiple">Peptide list from your history</option> 173 <option value="multiple">Peptide list from your history</option>
229 <option value="4">4</option> 225 <option value="4">4</option>
230 <option value="5">5</option> 226 <option value="5">5</option>
231 <option value="6">6</option> 227 <option value="6">6</option>
232 </param> 228 </param>
233 </when> 229 </when>
234 <!-- these are not working with pepquery version 1.6
235 <when value="3">
236 <param name="input" type="data" format="vcf" label="VCF File" argument="-i" help="" />
237 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the VCF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
238 </when>
239 <when value="4">
240 <param name="input" type="data" format="bed" label="BED File" argument="-i" help="" />
241 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the BED file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
242 </when>
243 <when value="5">
244 <param name="input" type="data" format="gtf" label="GTF File" argument="-i" help="" />
245 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the GTF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
246 </when>
247 -->
248 </conditional> 230 </conditional>
249 <conditional name="db_type"> 231 <conditional name="db_type">
250 <param name="db_type_selector" type="select" label="Protein Reference Database from" help="" > 232 <param name="db_type_selector" type="select" label="Protein Reference Database from" help="" >
251 <option value="history">history</option> 233 <option value="history">history</option>
252 <option value="download">download</option> 234 <option value="download">download</option>
452 </data> 434 </data>
453 435
454 </outputs> 436 </outputs>
455 <tests> 437 <tests>
456 <!-- Test-1 PepQueryDB peptide gencode:human --> 438 <!-- Test-1 PepQueryDB peptide gencode:human -->
457 <test> 439 <test expect_num_outputs="2">
458 <conditional name="validation"> 440 <conditional name="validation">
459 <param name="task_type" value="novel"/> 441 <param name="task_type" value="novel"/>
460 </conditional> 442 </conditional>
461 <section name="req_inputs"> 443 <section name="req_inputs">
462 <conditional name="input_type"> 444 <conditional name="input_type">
511 <output name="psm_rank_txt"> 493 <output name="psm_rank_txt">
512 <assert_contents> 494 <assert_contents>
513 <has_text text="LVVVGADGVGK" /> 495 <has_text text="LVVVGADGVGK" />
514 <not_has_text text="AHSSMVGVNLPQK" /> 496 <not_has_text text="AHSSMVGVNLPQK" />
515 <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" /> 497 <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
498 <has_n_columns n="22" />
516 </assert_contents> 499 </assert_contents>
517 </output> 500 </output>
518 <output name="log_txt"> 501 <output name="log_txt">
519 <assert_contents> 502 <assert_contents>
520 <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" /> 503 <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" />
521 </assert_contents> 504 </assert_contents>
522 </output> 505 </output>
523 </test> 506 </test>
524 507
525 <!-- Test-2 PepQueryDB peptide gencode:human pep.txt --> 508 <!-- Test-2 PepQueryDB peptide gencode:human pep.txt -->
526 <test> 509 <test expect_num_outputs="2">
527 <conditional name="validation"> 510 <conditional name="validation">
528 <param name="task_type" value="novel"/> 511 <param name="task_type" value="novel"/>
529 </conditional> 512 </conditional>
530 <section name="req_inputs"> 513 <section name="req_inputs">
531 <conditional name="input_type"> 514 <conditional name="input_type">
580 <output name="psm_rank_txt"> 563 <output name="psm_rank_txt">
581 <assert_contents> 564 <assert_contents>
582 <has_text text="LVVVGADGVGK" /> 565 <has_text text="LVVVGADGVGK" />
583 <not_has_text text="AHSSMVGVNLPQK" /> 566 <not_has_text text="AHSSMVGVNLPQK" />
584 <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" /> 567 <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
568 <has_n_columns n="22" />
585 </assert_contents> 569 </assert_contents>
586 </output> 570 </output>
587 <output name="log_txt"> 571 <output name="log_txt">
588 <assert_contents> 572 <assert_contents>
589 <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" /> 573 <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" />
590 </assert_contents> 574 </assert_contents>
591 </output> 575 </output>
592 </test> 576 </test>
593 577
594 <!-- Test-3 MGF peptide Uniprot.fasta --> 578 <!-- Test-3 MGF peptide Uniprot.fasta -->
595 <test> 579 <test expect_num_outputs="2">
596 <conditional name="validation"> 580 <conditional name="validation">
597 <param name="task_type" value="novel"/> 581 <param name="task_type" value="novel"/>
598 </conditional> 582 </conditional>
599 <section name="req_inputs"> 583 <section name="req_inputs">
600 <conditional name="input_type"> 584 <conditional name="input_type">
650 </section> 634 </section>
651 </section> 635 </section>
652 <output name="psm_rank_txt"> 636 <output name="psm_rank_txt">
653 <assert_contents> 637 <assert_contents>
654 <has_text text="ELGSSDLTAR" /> 638 <has_text text="ELGSSDLTAR" />
655 </assert_contents>
656 </output>
657 <output name="psm_rank_txt">
658 <assert_contents>
659 <has_text text="ELGSSDLTAR" />
660 <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+"/> 639 <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+"/>
640 <has_n_columns n="22" />
661 </assert_contents> 641 </assert_contents>
662 </output> 642 </output>
663 </test> 643 </test>
664 644
665 <!-- Test-4 PepQueryDB known peptide gencode:human pep.txt --> 645 <!-- Test-4 PepQueryDB known peptide gencode:human pep.txt -->
666 <test> 646 <test expect_num_outputs="2">
667 <conditional name="validation"> 647 <conditional name="validation">
668 <param name="task_type" value="known"/> 648 <param name="task_type" value="known"/>
669 </conditional> 649 </conditional>
670 <section name="req_inputs"> 650 <section name="req_inputs">
671 <conditional name="input_type"> 651 <conditional name="input_type">
690 </section> 670 </section>
691 <output name="psm_rank_txt"> 671 <output name="psm_rank_txt">
692 <assert_contents> 672 <assert_contents>
693 <has_text text="AHSSMVGVNLPQK" /> 673 <has_text text="AHSSMVGVNLPQK" />
694 <has_text text="6CPTAC_LUAD_W_BI_20180718_KL_f12:20286:3" /> 674 <has_text text="6CPTAC_LUAD_W_BI_20180718_KL_f12:20286:3" />
675 <has_n_columns n="22" />
695 </assert_contents> 676 </assert_contents>
696 </output> 677 </output>
697 </test> 678 </test>
698 679
699 </tests> 680 </tests>