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comparison normalize_select_features_scale.xml @ 1:6bccf5f85f92 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
author iuc
date Tue, 05 Nov 2024 11:54:52 +0000
parents c3170652bd98
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0:c3170652bd98 1:6bccf5f85f92
1 <tool id="seurat_preprocessing" name="Seurat Preprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="seurat_preprocessing" name="Seurat Preprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>- Normalize, Find Variable Features, Scale and Regress</description> 2 <description>- Normalize, Find Variable Features, Scale and Regress</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 @CMD@ 10 @CMD@
10 ]]></command> 11 ]]></command>
402 </tests> 403 </tests>
403 <help><![CDATA[ 404 <help><![CDATA[
404 Seurat 405 Seurat
405 ====== 406 ======
406 407
407 Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. 408 Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data.
408 409
409 Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. 410 Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.
410 411
411 NormalizeData 412 NormalizeData
412 ============= 413 =============
442 <https://satijalab.org/seurat/reference/findvariablefeatures>`__ 443 <https://satijalab.org/seurat/reference/findvariablefeatures>`__
443 444
444 Scale and regress the data with ScaleData 445 Scale and regress the data with ScaleData
445 ========================================= 446 =========================================
446 447
447 Scale and center features in the dataset. 448 Scale and center features in the dataset.
448 449
449 If variables are provided in vars.to.regress, they are individually regressed against each feature, and the resulting residuals are then scaled and centered. 450 If variables are provided in vars.to.regress, they are individually regressed against each feature, and the resulting residuals are then scaled and centered.
450 451
451 More details on the `seurat documentation 452 More details on the `seurat documentation
452 <https://satijalab.org/seurat/reference/scaledata>`__ 453 <https://satijalab.org/seurat/reference/scaledata>`__
453 454
454 SCTransform 455 SCTransform
455 =========== 456 ===========
456 457
457 Use this function as an alternative to the NormalizeData, FindVariableFeatures, ScaleData workflow. 458 Use this function as an alternative to the NormalizeData, FindVariableFeatures, ScaleData workflow.
458 459
459 Results are saved in a new assay (named SCT by default) with counts being (corrected) counts, data being log1p(counts), scale.data being pearson residuals; sctransform::vst intermediate results are saved in misc slot of new assay. 460 Results are saved in a new assay (named SCT by default) with counts being (corrected) counts, data being log1p(counts), scale.data being pearson residuals; sctransform::vst intermediate results are saved in misc slot of new assay.
460 461
461 More details on the `seurat documentation 462 More details on the `seurat documentation
462 <https://satijalab.org/seurat/reference/sctransform>`__ 463 <https://satijalab.org/seurat/reference/sctransform>`__