Mercurial > repos > lecorguille > xcms_xcmsset

comparison abims_xcms_xcmsSet.xml @ 38:e66eeca443e4 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
author lecorguille
date Wed, 05 Sep 2018 05:56:32 -0400
parents 9ada611dd63f
children e8d7395a70b2
comparison
equal deleted inserted replaced
37:9ada611dd63f 38:e66eeca443e4
406 Workflow position 406 Workflow position
407 ----------------- 407 -----------------
408 408
409 **Upstream tools** 409 **Upstream tools**
410 410
411 ========================= ================= ============================== ========== 411 ========================= ================= ==============================
412 Name output file format parameter 412 Name Output file Format
413 ========================= ================= ============================== ========== 413 ========================= ================= ==============================
414 MSnbase readMSData raw.RData rdata.msnbase.raw RData file 414 MSnbase.readMSData ``*``.raw.RData rdata.msnbase.raw
415 ========================= ================= ============================== ========== 415 ========================= ================= ==============================
416 416
417 417
418 **Downstream tools** 418 **Downstream tools**
419 419
420 =========================== ==================== ================= 420 ==================================== ======================== =========================
421 Name Output file Format 421 Name Output file Format
422 =========================== ==================== ================= 422 ==================================== ======================== =========================
423 xcms.group xset.RData rdata.xcms.raw 423 xcms.findChromPeaks Merger (single) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
424 --------------------------- -------------------- ----------------- 424 ------------------------------------ ------------------------ -------------------------
425 PCA ellipsoid by factors sampleMetadata.tsv Tabular 425 xcms.groupChromPeaks (zip) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
426 --------------------------- -------------------- ----------------- 426 ==================================== ======================== =========================
427 Anova sampleMetadata.tsv Tabular
428 =========================== ==================== =================
429 427
430 428
431 **Example of a metabolomic workflow** 429 **Example of a metabolomic workflow**
432 430
433 .. image:: xcms_xcmsset_workflow.png 431 .. image:: xcms_xcmsset_workflow.png
472 470
473 ------------ 471 ------------
474 Output files 472 Output files
475 ------------ 473 ------------
476 474
477 sampleMetadata.tsv
478
479 | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
480 | This file is necessary in the Anova and PCA step of the workflow.
481
482 xset.RData: rdata.xcms.findchrompeaks format 475 xset.RData: rdata.xcms.findchrompeaks format
483 476
484 | RData file that is necessary in the second step of the workflow "xcms.group". 477 | (single) RData files that is necessary in the second step of the workflow "xcms.groupChromPeaks" must to be merged using "xcms.findChromPeaks Merger"
478 | (zip) RData file that is necessary in the second step of the workflow "xcms.groupChromPeaks".
485 479
486 --------------------------------------------------- 480 ---------------------------------------------------
487 481
488 Changelog/News 482 Changelog/News
489 -------------- 483 --------------