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comparison bioconductor_scp.xml @ 1:8a6c7302de66 draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit 01a6a2434c6e77b5061ada328d849a4ad7c30529
author recetox
date Thu, 14 Aug 2025 13:41:01 +0000
parents cd2f3a280463
children
comparison
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0:cd2f3a280463 1:8a6c7302de66
1 <tool id="bioconductor_scp" name="bioconductor-scp" version="@TOOL_VERSION@+galaxy0" profile="23.0"> 1 <tool id="bioconductor_scp" name="bioconductor-scp" version="@TOOL_VERSION@+galaxy1" profile="23.0">
2 <description>single cell proteomics data analysis workflow</description> 2 <description>single cell proteomics data analysis workflow</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <import>help.xml</import> 5 <import>help.xml</import>
6 </macros> 6 </macros>
415 <tests> 415 <tests>
416 <test expect_num_outputs='2'> 416 <test expect_num_outputs='2'>
417 <param name="input_data" value="evidence_subset.txt"/> 417 <param name="input_data" value="evidence_subset.txt"/>
418 <param name="input_annotations" value="sampleAnnotation.txt"/> 418 <param name="input_annotations" value="sampleAnnotation.txt"/>
419 <param name="runcol" value="19"/> 419 <param name="runcol" value="19"/>
420 <param name="single_cells" value="Macrophage,Monocyte"/> 420 <section name="filtering_data">
421 <param name="samples_to_keep" value="Macrophage,Monocyte,Blank"/> 421 <param name="single_cells" value="Macrophage,Monocyte"/>
422 <param name="batch_col" value="2"/> 422 </section>
423 <param name="column_aggregation_peptides" value="6"/> 423 <section name="peptide_filtering">
424 <param name="column_aggregation_proteins" value="17"/> 424 <param name="samples_to_keep" value="Macrophage,Monocyte,Blank"/>
425 <param name="pca_coloring" value="4"/> 425 </section>
426 <section name="batch_correction">
427 <conditional name="select_batch_correction">
428 <param name="batch_col" value="2"/>
429 </conditional>
430 </section>
431 <section name="peptide_aggregation">
432 <param name="column_aggregation_peptides" value="6"/>
433 </section>
434 <section name="protein_aggregation">
435 <param name="column_aggregation_proteins" value="17"/>
436 </section>
437 <section name="dimensionality_reduction">
438 <conditional name="PCA_computation">
439 <param name="pca_coloring" value="4"/>
440 </conditional>
441 </section>
426 <output name="Processed_data"> 442 <output name="Processed_data">
427 <assert_contents> 443 <assert_contents>
428 <has_n_lines n="90"/> 444 <has_n_lines n="90"/>
429 <has_text text="E9PAV3"/> 445 <has_text text="E9PAV3"/>
430 <has_size size="625000" delta="20"/> 446 <has_size size="625000" delta="20"/>
433 </test> 449 </test>
434 <test expect_num_outputs='2'> 450 <test expect_num_outputs='2'>
435 <param name="input_data" value="evidence_subset.txt" /> 451 <param name="input_data" value="evidence_subset.txt" />
436 <param name="input_annotations" value="sampleAnnotation.txt"/> 452 <param name="input_annotations" value="sampleAnnotation.txt"/>
437 <param name="runcol" value="19"/> 453 <param name="runcol" value="19"/>
438 <param name="single_cells" value="Macrophage,Monocyte"/> 454 <section name="filtering_data">
439 <param name="samples_to_keep" value="Macrophage,Monocyte,Blank"/> 455 <param name="single_cells" value="Macrophage,Monocyte"/>
440 <param name="batch_col" value="2"/> 456 </section>
441 <param name="column_aggregation_peptides" value="6"/> 457 <section name="peptide_filtering">
442 <param name="column_aggregation_proteins" value="17"/> 458 <param name="samples_to_keep" value="Macrophage,Monocyte,Blank"/>
443 <param name="pca_coloring" value="4"/> 459 </section>
460 <section name="batch_correction">
461 <conditional name="select_batch_correction">
462 <param name="batch_col" value="2"/>
463 </conditional>
464 </section>
465 <section name="peptide_aggregation">
466 <param name="column_aggregation_peptides" value="6"/>
467 </section>
468 <section name="protein_aggregation">
469 <param name="column_aggregation_proteins" value="17"/>
470 </section>
471 <section name="dimensionality_reduction">
472 <conditional name="PCA_computation">
473 <param name="pca_coloring" value="4"/>
474 </conditional>
475 </section>
444 <output_collection name="plots" type="list"> 476 <output_collection name="plots" type="list">
445 <element name="PCA" file="PCA.pdf" ftype="pdf" compare="sim_size" delta="60"/> 477 <element name="PCA" file="PCA.pdf" ftype="pdf" compare="sim_size" delta="60"/>
446 <element name="QC_boxplot_peptide" file="QC_boxplot_peptide.pdf" ftype="pdf" compare="sim_size" delta="40"/> 478 <element name="QC_boxplot_peptide" file="QC_boxplot_peptide.pdf" ftype="pdf" compare="sim_size" delta="40"/>
447 <element name="QC_boxplot_peptide_norm" file="QC_boxplot_peptide_norm.pdf" ftype="pdf" compare="sim_size" delta="40"/> 479 <element name="QC_boxplot_peptide_norm" file="QC_boxplot_peptide_norm.pdf" ftype="pdf" compare="sim_size" delta="40"/>
448 <element name="QC_boxplot_protein" file="QC_boxplot.pdf" ftype="pdf" compare="sim_size" delta="40"/> 480 <element name="QC_boxplot_protein" file="QC_boxplot.pdf" ftype="pdf" compare="sim_size" delta="40"/>
463 </test> 495 </test>
464 <test expect_num_outputs='3'> 496 <test expect_num_outputs='3'>
465 <param name="input_data" value="evidence_subset.txt" /> 497 <param name="input_data" value="evidence_subset.txt" />
466 <param name="input_annotations" value="sampleAnnotation.txt"/> 498 <param name="input_annotations" value="sampleAnnotation.txt"/>
467 <param name="runcol" value="19"/> 499 <param name="runcol" value="19"/>
468 <param name="single_cells" value="Macrophage,Monocyte"/> 500 <section name="filtering_data">
469 <param name="samples_to_keep" value="Macrophage,Monocyte,Blank"/> 501 <param name="single_cells" value="Macrophage,Monocyte"/>
470 <param name="column_aggregation_peptides" value="6"/> 502 </section>
471 <param name="column_aggregation_proteins" value="17"/> 503 <section name="peptide_filtering">
472 <param name="batch_col" value="2"/> 504 <param name="samples_to_keep" value="Macrophage,Monocyte,Blank"/>
473 <param name="export_tables" value="true"/> 505 </section>
474 <param name="pca_coloring" value="4"/> 506 <section name="peptide_aggregation">
507 <param name="column_aggregation_peptides" value="6"/>
508 </section>
509 <section name="protein_aggregation">
510 <param name="column_aggregation_proteins" value="17"/>
511 </section>
512 <section name="batch_correction">
513 <conditional name="select_batch_correction">
514 <param name="batch_col" value="2"/>
515 </conditional>
516 </section>
517 <section name="data_export">
518 <param name="export_tables" value="true"/>
519 </section>
520 <section name="dimensionality_reduction">
521 <conditional name="PCA_computation">
522 <param name="pca_coloring" value="4"/>
523 </conditional>
524 </section>
475 <output_collection name="intermediate_outputs" type="list" count="6"/> 525 <output_collection name="intermediate_outputs" type="list" count="6"/>
476 <output name="Processed_data"> 526 <output name="Processed_data">
477 <assert_contents> 527 <assert_contents>
478 <has_size size="625000" delta="20"/> 528 <has_size size="625000" delta="20"/>
479 <has_n_lines n="90"/> 529 <has_n_lines n="90"/>
483 </test> 533 </test>
484 <test expect_num_outputs='4'> 534 <test expect_num_outputs='4'>
485 <param name="input_data" value="evidence_subset.txt" /> 535 <param name="input_data" value="evidence_subset.txt" />
486 <param name="input_annotations" value="sampleAnnotation.txt"/> 536 <param name="input_annotations" value="sampleAnnotation.txt"/>
487 <param name="runcol" value="19"/> 537 <param name="runcol" value="19"/>
488 <param name="single_cells" value="Macrophage,Monocyte"/> 538 <section name="filtering_data">
489 <param name="samples_to_keep" value="Macrophage,Monocyte,Blank"/> 539 <param name="single_cells" value="Macrophage,Monocyte"/>
490 <param name="batch_col" value="2"/> 540 </section>
491 <param name="export_RData" value="TRUE"/> 541 <section name="peptide_filtering">
492 <param name="export_R_script" value="TRUE"/> 542 <param name="samples_to_keep" value="Macrophage,Monocyte,Blank"/>
493 <param name="column_aggregation_peptides" value="6"/> 543 </section>
494 <param name="column_aggregation_proteins" value="17"/> 544 <section name="batch_correction">
495 <param name="pca_coloring" value="4"/> 545 <conditional name="select_batch_correction">
546 <param name="batch_col" value="2"/>
547 </conditional>
548 </section>
549 <section name="peptide_aggregation">
550 <param name="column_aggregation_peptides" value="6"/>
551 </section>
552 <section name="protein_aggregation">
553 <param name="column_aggregation_proteins" value="17"/>
554 </section>
555 <section name="data_export">
556 <param name="export_RData" value="TRUE"/>
557 <param name="export_R_script" value="TRUE"/>
558 </section>
559 <section name="dimensionality_reduction">
560 <conditional name="PCA_computation">
561 <param name="pca_coloring" value="4"/>
562 </conditional>
563 </section>
496 <output name="Processed_data"> 564 <output name="Processed_data">
497 <assert_contents> 565 <assert_contents>
498 <has_size size="625000" delta="20"/> 566 <has_size size="625000" delta="20"/>
499 <has_n_lines n="90"/> 567 <has_n_lines n="90"/>
500 <has_text text="E9PAV3"/> 568 <has_text text="E9PAV3"/>