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comparison inspect_and_manipulate.xml @ 1:4ec52a83ec82 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 11:55:01 +0000
parents 50c5abeb08ba
children
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0:50c5abeb08ba 1:4ec52a83ec82
1 <tool id="seurat_data" name="Seurat Data Management" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="seurat_data" name="Seurat Data Management" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>- Inspect and Manipulate </description> 2 <description>- Inspect and Manipulate </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>
52 col.names = TRUE 53 col.names = TRUE
53 @CMD_inspect_rds_outputs@ 54 @CMD_inspect_rds_outputs@
54 55
55 #else if $method.inspect.inspect == 'Matrix' 56 #else if $method.inspect.inspect == 'Matrix'
56 inspect<-LayerData( 57 inspect<-LayerData(
57 seurat_obj, 58 seurat_obj,
58 assay='$method.inspect.assay', 59 assay='$method.inspect.assay',
59 layer='$method.inspect.layer' 60 layer='$method.inspect.layer'
60 ) 61 )
61 row.names = TRUE 62 row.names = TRUE
62 col.names = TRUE 63 col.names = TRUE
63 @CMD_inspect_rds_outputs@ 64 @CMD_inspect_rds_outputs@
670 </tests> 671 </tests>
671 <help><![CDATA[ 672 <help><![CDATA[
672 Seurat 673 Seurat
673 ====== 674 ======
674 675
675 Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. 676 Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data.
676 677
677 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. 678 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.
678 679
679 Inspect and Manipulate 680 Inspect and Manipulate
680 ====================== 681 ======================
715 =========== 716 ===========
716 717
717 Merge 718 Merge
718 ===== 719 =====
719 720
720 Combine two Seurat Objects into a single Seurat Object. 721 Combine two Seurat Objects into a single Seurat Object.
721 Each object will be placed in a separate layer, but you can choose to run the JoinLayers function after merging to combine the objects into a single layer. 722 Each object will be placed in a separate layer, but you can choose to run the JoinLayers function after merging to combine the objects into a single layer.
722 723
723 Subset 724 Subset
724 ====== 725 ======
725 726
726 Subset a group of cells based on their ident or another grouping in your cell metadata. 727 Subset a group of cells based on their ident or another grouping in your cell metadata.
727 728
728 DietSeurat 729 DietSeurat
729 ========== 730 ==========
730 731
731 Keep only certain aspects of the Seurat object. 732 Keep only certain aspects of the Seurat object.
732 Can be useful in functions that utilize merge as it reduces the amount of data in the merge 733 Can be useful in functions that utilize merge as it reduces the amount of data in the merge
733 734
734 More details on these essential commands can be found in the `seurat documentation 735 More details on these essential commands can be found in the `seurat documentation
735 <https://satijalab.org/seurat/reference/dietseurat>`__ 736 <https://satijalab.org/seurat/reference/dietseurat>`__
736 737
737 AggregateExpression 738 AggregateExpression
738 =================== 739 ===================
739 740
740 Returns summed counts ("pseudobulk") for each identity class. 741 Returns summed counts ("pseudobulk") for each identity class.
741 742
742 More details on the `seurat documentation 743 More details on the `seurat documentation
743 <https://satijalab.org/seurat/reference/aggregateexpression>`__ 744 <https://satijalab.org/seurat/reference/aggregateexpression>`__
744 745
745 746
746 DefaultAssay 747 DefaultAssay
747 ============ 748 ============
748 749
749 Set the default assay for multimodal data. 750 Set the default assay for multimodal data.
750 751
751 You can use the Inspect - General function to check which assay is currently active and which other assays are available. 752 You can use the Inspect - General function to check which assay is currently active and which other assays are available.
752 753
753 ]]></help> 754 ]]></help>
754 <expand macro="citations"/> 755 <expand macro="citations"/>